dbMatrix::t(dense)
-## connection : /tmp/RtmpMqGvht/file2228112b0dda.duckdb
+## connection : /tmp/RtmpNLoJMo/file180317474a4a.duckdb
## table name : 'dense_test'
## 50 x 50 matrix of class "dbDenseMatrix"
## [[ Colnames 'row1', 'row2', 'row3' ... suppressing 44 ...'row48', 'row49', 'row50' ]]
diff --git a/pkgdown.yml b/pkgdown.yml
index 0d30579..4c5f509 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
arithmetic: arithmetic.html
operations: operations.html
overview: overview.html
-last_built: 2024-07-11T20:00Z
+last_built: 2024-07-12T16:53Z
urls:
reference: https://drieslab.github.io/dbMatrix/reference
article: https://drieslab.github.io/dbMatrix/articles
diff --git a/search.json b/search.json
index 193a8f5..8666c3f 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"get-test-data","dir":"Articles","previous_headings":"","what":"Get test data","title":"Arithmetic","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object. file contains 634 rows 624 columns. rows represent gene names columns represent cell names. values integers represent number times gene detected cell. Like single-cell RNA-seq data, matrix sparse.","code":"dgc <- readRDS(\"../data/dgc.rds\") dplyr::glimpse(dgc) #> Loading required package: Matrix #> #> Attaching package: 'Matrix' #> The following object is masked from 'package:dbMatrix': #> #> readMM #> Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots #> ..@ i : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... #> ..@ p : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... #> ..@ Dim : int [1:2] 634 624 #> ..@ Dimnames:List of 2 #> .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... #> .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... #> ..@ x : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... #> ..@ factors : list()"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"create-a-dbmatrix-object","dir":"Articles","previous_headings":"","what":"Create a dbMatrix object","title":"Arithmetic","text":"Let’s create dbSparseMatrix object dgc object.","code":"# Note: by default the constructor creates a dbMatrix object in-memory con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\") dbsm <- createDBMatrix(value = dgc, con = con, name = 'visium', class = \"dbSparseMatrix\", overwrite = TRUE) # preview the object dbsm #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> #> Gna12 1 2 1 1 9 1 3 5 3 . #> Ccnd2 . 1 1 . . 1 . 1 1 . #> Btbd17 . 1 1 1 . . 2 . . . #> #> ......suppressing 614 columns and 628 rows #> #> Gm19935 . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"scalar-arithmetic","dir":"Articles","previous_headings":"","what":"Scalar Arithmetic","title":"Arithmetic","text":"dbMatrix emulates scalar arithmetic Matrix package. Note: Addition subtraction non-zero addends dbSparseMatrix results dbDenseMatrix.","code":"dbsm + 1 #> Warning in toDbDense(dbm): Densifying dbSparseMatrix on the fly. See #> ?precompute to speed up densification. #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbDenseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> 1 2 3 … 622 623 624 #> 1 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> 2 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> 3 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ #> 632 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> 633 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> 634 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 dbsm * 100 #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> #> Gna12 100 200 100 100 900 100 300 500 300 . #> Ccnd2 . 100 100 . . 100 . 100 100 . #> Btbd17 . 100 100 100 . . 200 . . . #> #> ......suppressing 614 columns and 628 rows #> #> Gm19935 . 100 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 100 . . . . . . . . 100"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-arithmetic","dir":"Articles","previous_headings":"","what":"Matrix Arithmetic","title":"Arithmetic","text":"dbMatrix also supports matrix arithmetic dbMatrix objects conformable.","code":"dbsm + dbsm #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> #> Gna12 2 4 2 2 18 2 6 10 6 . #> Ccnd2 . 2 2 . . 2 . 2 2 . #> Btbd17 . 2 2 2 . . 4 . . . #> #> ......suppressing 614 columns and 628 rows #> #> Gm19935 . 2 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 2 . . . . . . . . 2"},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"hadamard-product","dir":"Articles","previous_headings":"Matrix Multiplication","what":"Hadamard product","title":"Arithmetic","text":"","code":"dbsm * dbsm #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> #> Gna12 1 4 1 1 81 1 9 25 9 . #> Ccnd2 . 1 1 . . 1 . 1 1 . #> Btbd17 . 1 1 1 . . 4 . . . #> #> ......suppressing 614 columns and 628 rows #> #> Gm19935 . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-product","dir":"Articles","previous_headings":"Matrix Multiplication","what":"Matrix product","title":"Arithmetic","text":"TODO","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"shutdown","dir":"Articles","previous_headings":"","what":"Shutdown","title":"Arithmetic","text":"","code":"dbMatrix::dbDisconnect(dbsm, shutdown = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Arithmetic","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #> #> Matrix products: default #> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 #> #> locale: #> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 #> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 #> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C #> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C #> #> time zone: UTC #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] Matrix_1.7-0 dbMatrix_0.0.0.9021 MatrixGenerics_1.16.0 #> [4] matrixStats_1.3.0 #> #> loaded via a namespace (and not attached): #> [1] bit_4.0.5 jsonlite_1.8.8 crayon_1.5.3 dplyr_1.1.4 #> [5] compiler_4.4.1 tidyselect_1.2.1 blob_1.2.4 jquerylib_0.1.4 #> [9] systemfonts_1.1.0 textshaping_0.4.0 yaml_2.3.9 fastmap_1.2.0 #> [13] lattice_0.22-6 R6_2.5.1 generics_0.1.3 knitr_1.48 #> [17] tibble_3.2.1 desc_1.4.3 DBI_1.2.3 bslib_0.7.0 #> [21] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 cachem_1.1.0 #> [25] xfun_0.45 fs_1.6.4 sass_0.4.9 bit64_4.0.5 #> [29] cli_3.6.3 withr_3.0.0 pkgdown_2.1.0 magrittr_2.0.3 #> [33] digest_0.6.36 grid_4.4.1 dbplyr_2.5.0 lifecycle_1.0.4 #> [37] vctrs_0.6.5 evaluate_0.24.0 glue_1.7.0 data.table_1.15.4 #> [41] duckdb_1.0.0-1 ragg_1.3.2 fansi_1.0.6 purrr_1.0.2 #> [45] rmarkdown_2.27 tools_4.4.1 pkgconfig_2.0.3 htmltools_0.5.8.1"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Operations","text":"vignette introduces generic functions operations supported dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"loading-library","dir":"Articles","previous_headings":"","what":"Loading library","title":"Operations","text":"","code":"library(dbMatrix) library(Matrix)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbmatrix-generics","dir":"Articles","previous_headings":"","what":"dbMatrix generics","title":"Operations","text":"dbMatrix subclasses currently support basic generic functions listed support operations coming soon.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"get-test-data","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Get test data","title":"Operations","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object.","code":"dgc <- readRDS(\"../data/dgc.rds\") dplyr::glimpse(dgc) ## Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots ## ..@ i : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... ## ..@ p : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... ## ..@ Dim : int [1:2] 634 624 ## ..@ Dimnames:List of 2 ## .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... ## .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... ## ..@ x : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... ## ..@ factors : list() # create dbSparseMatrix from the same dgc con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\") sparse <- createDBMatrix(value = dgc, con = con, name = 'visium', class = \"dbSparseMatrix\", overwrite = TRUE) # preview # show function aims to emulate the show method for dgCMatrix head(sparse) ## connection : :memory: ## table name : 'visium' ## 6 x 624 matrix of class \"dbSparseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ## ## Gna12 1 2 1 1 9 1 3 5 3 . ## [ reached getOption(\"max.print\") -- omitted 633 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(sparse) ## connection : :memory: ## table name : 'visium' ## 624 x 634 matrix of class \"dbSparseMatrix\" ## [[ Colnames 'Gna12', 'Ccnd2', 'Btbd17' ... suppressing 628 ...'Gm19935', '9630013A20Rik', '2900040C04Rik' ]] ## ## AAAGGGATGTAGCAAG-1 1 . . . . . 1 . . . ## [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ## ## ......suppressing 624 columns and 618 rows ## ## NA ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(sparse) ## AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1 ## 0.7413249 1.3296530 1.1435331 0.8343849 ## AACAACTGGTAGTTGC-1 AACAGGAAATCGAATA-1 AACAGGATGGGCCGCG-1 AACCATGGGATCGCTA-1 ## 1.6135647 2.2129338 1.7223975 1.9022082 ## AACCCAGAGACGGAGA-1 AACCGAGCTTGGTCAT-1 ## 0.7397476 0.9258675 ## [ reached getOption(\"max.print\") -- omitted 614 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(sparse) ## AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1 ## 470 843 725 529 ## AACAACTGGTAGTTGC-1 AACAGGAAATCGAATA-1 AACAGGATGGGCCGCG-1 AACCATGGGATCGCTA-1 ## 1023 1403 1092 1206 ## AACCCAGAGACGGAGA-1 AACCGAGCTTGGTCAT-1 ## 469 587 ## [ reached getOption(\"max.print\") -- omitted 614 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(sparse) ## Gna12 Ccnd2 Btbd17 Sox9 Sez6 Serpinf1 S100a6 Col1a1 ## 2.7179487 1.7323718 0.5528846 0.8766026 4.4679487 0.3092949 1.6522436 0.1185897 ## Vwf Esam ## 0.6346154 0.4391026 ## [ reached getOption(\"max.print\") -- omitted 624 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(sparse) ## Gna12 Ccnd2 Btbd17 Sox9 Sez6 Serpinf1 S100a6 Col1a1 ## 1696 1081 345 547 2788 193 1031 74 ## Vwf Esam ## 396 274 ## [ reached getOption(\"max.print\") -- omitted 624 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"dim","title":"Operations","text":"","code":"dim(sparse) ## [1] 634 624 dim(dgc) ## [1] 634 624"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"check-results-are-equivalent","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Check results are equivalent","title":"Operations","text":"","code":"all.equal(dbMatrix::colMeans(sparse), Matrix::colMeans(dgc)) ## [1] TRUE all.equal(dbMatrix::colSums(sparse), Matrix::colSums(dgc)) ## [1] TRUE all.equal(dbMatrix::rowMeans(sparse), Matrix::rowMeans(dgc)) ## [1] TRUE all.equal(dbMatrix::rowSums(sparse), Matrix::rowSums(dgc)) ## [1] TRUE"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbdensematrix-operations","dir":"Articles","previous_headings":"","what":"dbDenseMatrix Operations","title":"Operations","text":"","code":"# below is a convenience function to simulate a dbDenseMatrix dense = dbMatrix::sim_dbDenseMatrix() # preview dense ## connection : /tmp/RtmpMqGvht/file2228112b0dda.duckdb ## table name : 'dense_test' ## 50 x 50 matrix of class \"dbDenseMatrix\" ## 1 2 3 … 48 49 50 ## 1 1.4e+00 3.2e-01 1.2e+00 … 2.2e-01 1.3e+00 -3.9e-01 ## 2 -5.6e-01 -7.8e-01 1.0e+00 … -1.1e-01 -6.0e-01 -9.9e-02 ## 3 3.6e-01 1.6e+00 -1.0e+00 … 2.0e-02 5.7e-02 -2.8e-02 ## ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ## 48 1.4e+00 -1.5e+00 -4.3e-01 … -7.4e-02 -3.5e-02 7.0e-01 ## 49 -4.3e-01 8.0e-02 7.0e-01 … -7.7e-01 -9.2e-01 -1.4e-01 ## 50 6.6e-01 6.5e-01 -1.1e+00 … 5.9e-01 1.1e+00 5.0e-01"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(dense) ## connection : /tmp/RtmpMqGvht/file2228112b0dda.duckdb ## table name : 'dense_test' ## 50 x 50 matrix of class \"dbDenseMatrix\" ## [[ Colnames 'row1', 'row2', 'row3' ... suppressing 44 ...'row48', 'row49', 'row50' ]] ## 1 2 3 … 48 49 50 ## 1 1.4e+00 -5.6e-01 3.6e-01 … 1.4e+00 -4.3e-01 6.6e-01 ## 2 3.2e-01 -7.8e-01 1.6e+00 … -1.5e+00 8.0e-02 6.5e-01 ## 3 1.2e+00 1.0e+00 -1.0e+00 … -4.3e-01 7.0e-01 -1.1e+00 ## ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ## 48 2.2e-01 -1.1e-01 2.0e-02 … -7.4e-02 -7.7e-01 5.9e-01 ## 49 1.3e+00 -6.0e-01 5.7e-02 … -3.5e-02 -9.2e-01 1.1e+00 ## 50 -3.9e-01 -9.9e-02 -2.8e-02 … 7.0e-01 -1.4e-01 5.0e-01"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(dense) ## col1 col2 col3 col4 col5 col6 ## -0.035671782 0.100701413 -0.151251089 -0.023716326 0.007939877 -0.028676220 ## col7 col8 col9 col10 ## -0.061541347 0.127414276 -0.119421148 -0.116239863 ## [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(dense) ## col1 col2 col3 col4 col5 col6 col7 ## -1.7835891 5.0350707 -7.5625544 -1.1858163 0.3969938 -1.4338110 -3.0770674 ## col8 col9 col10 ## 6.3707138 -5.9710574 -5.8119931 ## [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(dense) ## row1 row2 row3 row4 row5 row6 ## 0.053643638 0.002494642 0.031334034 0.093889009 -0.048311439 -0.047287825 ## row7 row8 row9 row10 ## 0.092209664 -0.023069981 0.096433464 -0.093495713 ## [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(dense) ## row1 row2 row3 row4 row5 row6 row7 ## 2.6821819 0.1247321 1.5667017 4.6944505 -2.4155720 -2.3643912 4.6104832 ## row8 row9 row10 ## -1.1534990 4.8216732 -4.6747857 ## [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"mean","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"mean","title":"Operations","text":"","code":"dbMatrix::mean(dense) ## [1] -0.009673541"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"dim","title":"Operations","text":"","code":"dim(dense) ## [1] 50 50"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"shutdown","dir":"Articles","previous_headings":"","what":"Shutdown","title":"Operations","text":"","code":"dbMatrix::dbDisconnect(dense, shutdown = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Operations","text":"","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## ## Matrix products: default ## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 ## ## locale: ## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 ## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 ## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C ## [10] LC_TELEPHONE=C ## [ reached getOption(\"max.print\") -- omitted 2 entries ] ## ## time zone: UTC ## tzcode source: system (glibc) ## ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: ## [1] Matrix_1.7-0 dbMatrix_0.0.0.9021 MatrixGenerics_1.16.0 ## [4] matrixStats_1.3.0 ## ## loaded via a namespace (and not attached): ## [1] jsonlite_1.8.8 crayon_1.5.3 dplyr_1.1.4 compiler_4.4.1 ## [5] tidyselect_1.2.1 blob_1.2.4 jquerylib_0.1.4 systemfonts_1.1.0 ## [9] textshaping_0.4.0 yaml_2.3.9 ## [ reached getOption(\"max.print\") -- omitted 36 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbmatrix","dir":"Articles","previous_headings":"","what":"dbMatrix","title":"Overview","text":"dbMatrix core package dbverse library inherits dbData base class consists two subclasses, dbSparseMatrix dbDenseMatrix. dbMatrix objects emulate -memory dense sparse matrices embedded database powered DuckDB.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbsparsematrix","dir":"Articles","previous_headings":"","what":"dbSparseMatrix","title":"Overview","text":"Sparse matrices represented triplet vectors , j, x numerical vectors. j refer row column indices, respectively, specific x values counts. Note: j vectors one-based following conventions Matrix R package TSparseMatrix class. dbSparseMatrix class stores triplet vector representation associated dimension names dimensions available. none provided, automatically generated factors (enums) row# col# labels rownames colnames, respectively. dbSparseMatrix class contain zeros triplet vector representation. Zero values inferred based provided dimensions. Support compressed sparse column matrices dgCMatrix class Matrix R package currently implemented. information sparse matrices, see wiki article .","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbdensematrix","dir":"Articles","previous_headings":"","what":"dbDenseMatrix","title":"Overview","text":"use approach dbSparseMatrix represent dense matrix triplet , j, x vector. difference dbDenseMatrix class consists values matrix, including zeros.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edward C. Ruiz. Author. Jiaji George Chen. Author. Ruben Dries. Author, maintainer.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"C. Ruiz E, George Chen J, Dries R (2024). dbMatrix: dbMatrix. R package version 0.0.0.9021, https://drieslab.github.io/dbMatrix/.","code":"@Manual{, title = {dbMatrix: dbMatrix}, author = {Edward {C. Ruiz} and Jiaji {George Chen} and Ruben Dries}, year = {2024}, note = {R package version 0.0.0.9021}, url = {https://drieslab.github.io/dbMatrix/}, }"},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"dbmatrix","dir":"","previous_headings":"","what":"dbMatrix","title":"dbMatrix","text":"dbMatrix core package dbverse library. goal dbMatrix support larger--memory matrix computations.","code":""},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"dbMatrix","text":"can install development version dbMatrix Github like :","code":"# install.packages(\"pak\", repos = sprintf(\"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch)) pak::pak(\"drieslab/dbMatrix\")"},{"path":"https://drieslab.github.io/dbMatrix/reference/DBI.html","id":null,"dir":"Reference","previous_headings":"","what":"dbDisconnect — dbDisconnect,dbMatrix-method","title":"dbDisconnect — dbDisconnect,dbMatrix-method","text":"dbDisconnect dbListTables","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/DBI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dbDisconnect — dbDisconnect,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' dbDisconnect(x, ...) # S4 method for class 'dbMatrix' dbListTables(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":null,"dir":"Reference","previous_headings":"","what":"Set a column to numeric — castNumeric","title":"Set a column to numeric — castNumeric","text":"Sets column numeric first checking column data type. nothing column already double precaution avoid truncation values.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set a column to numeric — castNumeric","text":"","code":"# S4 method for class 'dbData,character' castNumeric(x, col, ...) # S4 method for class 'dbMatrix,missing' castNumeric(x, col, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set a column to numeric — castNumeric","text":"x dbData data object col column cast numeric ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Column data types of dbData objects — colTypes","title":"Column data types of dbData objects — colTypes","text":"Get column data types objects inherit 'dbData'","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Column data types of dbData objects — colTypes","text":"","code":"# S4 method for class 'dbData' colTypes(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Column data types of dbData objects — colTypes","text":"x dbData data object ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a sparse or dense dbMatrix object — createDBMatrix","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"Create S4 dbMatrix object sparse dense triplet vector format.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"","code":"createDBMatrix( value, class = NULL, con = NULL, overwrite = FALSE, name = \"dbMatrix\", dims = NULL, dim_names = NULL, mtx_rowname_file_path, mtx_rowname_col_idx = 1, mtx_colname_file_path, mtx_colname_col_idx = 1, ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"value data added database. See details supported data types (required) class class dbMatrix: dbDenseMatrix dbSparseMatrix (required) con DBI duckdb connection object (required) overwrite whether overwrite table already exists database (required) name table name assign within database (optional, default: \"dbMatrix\") dims dimensions matrix (optional: [int, int]) dim_names dimension names matrix (optional: list(enum, enum)) mtx_rowname_file_path path .mtx rowname file read (optional) database. default, header assumed. mtx_rowname_col_idx column index row name file (optional) mtx_colname_file_path path .mtx colname file read database. default, header assumed. (optional) mtx_colname_col_idx column index column name file (optional) ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"function reads data pre-existing DuckDB database. Based name db_path lazy connection made downstream dbMatrix initialization. Supported value data types: dgCMatrix -memory sparse matrix Matrix package dgTMatrix -memory triplet vector COO matrix matrix -memory dense matrix base R .mtx Path .mtx file (TODO) .csv Path .csv file (TODO) tbl_duckdb_connection Table DuckDB database ijx format existing dbMatrix object. dims dim_names must specified value tbl_duckdb_connection.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"","code":"dgc <- dbMatrix:::sim_dgc() #> Error in as(data, \"dgCMatrix\"): no method or default for coercing “matrix” to “dgCMatrix” dbSparse <- createDBMatrix(value = dgc, db_path = \":memory:\", name = \"sparse_matrix\", class = \"dbSparseMatrix\", overwrite = TRUE) #> Error in eval(expr, envir, enclos): object 'dgc' not found dbSparse #> Error in eval(expr, envir, enclos): object 'dbSparse' not found"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDataFrame-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dbDataFrame class — dbDataFrame-class","title":"S4 dbDataFrame class — dbDataFrame-class","text":"Representation dataframes using -disk database. object used connection single table exists within database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDataFrame-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dbDataFrame class — dbDataFrame-class","text":"data dplyr tbl represents database data hash unique hash ID backend remote_name name table within database contains data key column set key ordering subsetting ","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDenseMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","title":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","text":"Representation dense matrices using -disk database. Inherits dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDenseMatrix-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","text":"data dense ijx dataframe/tibble","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dbMatrix class — dbMatrix-class","title":"S4 dbMatrix class — dbMatrix-class","text":"Representation sparse matrices using -disk database. object used connection single table exists within database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dbMatrix class — dbMatrix-class","text":"dim_names row [1] col [2] names dims dimensions matrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbSparseMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 Class for dbSparseMatrix — dbSparseMatrix-class","title":"S4 Class for dbSparseMatrix — dbSparseMatrix-class","text":"Representation sparse matrices using -disk database. Inherits dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for conn arg — .check_con","title":"Input validation for conn arg — .check_con","text":"Input validation conn arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for conn arg — .check_con","text":"","code":".check_con(conn)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Input validation for conn arg — .check_con","text":"conn tbl_duckdb_connection object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for name arg — .check_name","title":"Input validation for name arg — .check_name","text":"Input validation name arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for name arg — .check_name","text":"","code":".check_name(name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_overwrite.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for overwrite arg — .check_overwrite","title":"Input validation for overwrite arg — .check_overwrite","text":"Input validation overwrite arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_overwrite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for overwrite arg — .check_overwrite","text":"","code":".check_overwrite(conn, overwrite, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for data arg — .check_value","title":"Input validation for data arg — .check_value","text":"Input validation data arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for data arg — .check_value","text":"","code":".check_value(value)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Input validation for data arg — .check_value","text":"x Matrix, matrix, tbl_duckdb_connection object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":null,"dir":"Reference","previous_headings":"","what":"flex_window_order — flex_window_order","title":"flex_window_order — flex_window_order","text":"workaround multiple dbplyr window column ordering","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"flex_window_order — flex_window_order","text":"","code":"flex_window_order(x, order_cols)"},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"flex_window_order — flex_window_order","text":"x dbplyr::tbl_lazy order_cols character vector column names","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":null,"dir":"Reference","previous_headings":"","what":"get_MM_dim — get_MM_dim","title":"get_MM_dim — get_MM_dim","text":"Internal function read dimensions .mtx file","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_MM_dim — get_MM_dim","text":"","code":"get_MM_dim(mtx_file_path)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_MM_dim — get_MM_dim","text":"mtx_file_path path .mtx file read database","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_MM_dim — get_MM_dim","text":"integer vector dimensions","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"get_MM_dim — get_MM_dim","text":"Scans header mtx file (starting representing dimensions number nonzero values. Note: header size can vary depending .mtx file.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":null,"dir":"Reference","previous_headings":"","what":"get_MM_dimnames — get_MM_dimnames","title":"get_MM_dimnames — get_MM_dimnames","text":"Internal function read row column names .mtx file","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_MM_dimnames — get_MM_dimnames","text":"","code":"get_MM_dimnames( mtx_file_path, mtx_rowname_file_path, mtx_rowname_col_idx = 1, mtx_colname_file_path, mtx_colname_col_idx = 1, ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_MM_dimnames — get_MM_dimnames","text":"mtx_file_path path .mtx file read database mtx_rowname_file_path path .mtx rowname file read database. default, header assumed. mtx_rowname_col_idx column index row name file mtx_colname_file_path path .mtx colname file read database. default, header assumed. mtx_colname_col_idx column index column name file ... additional params pass data.table::fread","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_MM_dimnames — get_MM_dimnames","text":"list row column name character vectors","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"get_MM_dimnames — get_MM_dimnames","text":"Can used read row column names .mtx files. Note: files must contain header (colnames). mtx_rowname_col_idx mtx_colname_col_idx can used specify column index row column name files, respectively. default, first column used . TODO: Support reading rownames colnames.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":null,"dir":"Reference","previous_headings":"","what":"get_con — get_con","title":"get_con — get_con","text":"get_con","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_con — get_con","text":"","code":"get_con(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_con — get_con","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":null,"dir":"Reference","previous_headings":"","what":"get_dbdir — get_dbdir","title":"get_dbdir — get_dbdir","text":"get_dbdir","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_dbdir — get_dbdir","text":"","code":"get_dbdir(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_dbdir — get_dbdir","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":null,"dir":"Reference","previous_headings":"","what":"get_tblName — get_tblName","title":"get_tblName — get_tblName","text":"get_tblName","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_tblName — get_tblName","text":"","code":"get_tblName(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_tblName — get_tblName","text":"dbData","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbDataFrame-method.html","id":null,"dir":"Reference","previous_headings":"","what":"head — head,dbDataFrame-method","title":"head — head,dbDataFrame-method","text":"head","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbDataFrame-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"head — head,dbDataFrame-method","text":"","code":"# S4 method for class 'dbDataFrame' head(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"head — head,dbMatrix-method","title":"head — head,dbMatrix-method","text":"head","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"head — head,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' head(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/hidden_aliases.html","id":null,"dir":"Reference","previous_headings":"","what":"rowSums — [,dbData,missing,missing,missing-method","title":"rowSums — [,dbData,missing,missing,missing-method","text":"rowSums rowSums colSums colSums rowMeans rowMeans colMeans colMeans colSds colSds rowSds rowSds mean mean log Transpose nrow ncol ncol ncol dim","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/hidden_aliases.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rowSums — [,dbData,missing,missing,missing-method","text":"","code":"# S4 method for class 'dbData,missing,missing,missing' x[i, j] # S4 method for class 'dbData,missing,missing,ANY' x[i, j] <- value # S4 method for class 'dbMatrix,dbIndex,missing,missing' x[i, j, ..., drop = TRUE] # S4 method for class 'dbMatrix,missing,dbIndex,missing' x[i, j, ..., drop = TRUE] # S4 method for class 'dbMatrix,dbIndex,dbIndex,missing' x[i, j, ..., drop = TRUE] # S4 method for class 'dbDataFrame,dbIndex,missing,ANY' x[i, j, ..., drop = TRUE] # S4 method for class 'dbDataFrame,missing,dbIndex,ANY' x[i, j, ..., drop = TRUE] # S4 method for class 'dbDataFrame,dbIndex,dbIndex,ANY' x[i, j, ..., drop = FALSE] # S4 method for class 'dbDataFrame,missing,missing,missing' x[i, j] # S4 method for class 'dbDataFrame,missing,missing,ANY' x[i, j] <- value # S4 method for class 'dbDataFrame' names(x) # S4 method for class 'dbDataFrame,dbIndex' names(x) <- value # S4 method for class 'dbData' rownames(x) # S4 method for class 'dbMatrix' rownames(x) # S4 method for class 'dbMatrix' rownames(x) <- value # S4 method for class 'dbData' colnames(x) # S4 method for class 'dbMatrix' colnames(x) # S4 method for class 'dbMatrix,ANY' colnames(x) <- value # S4 method for class 'dbDataFrame,dbIndex' colnames(x) <- value # S4 method for class 'dbMatrix' dimnames(x) # S4 method for class 'dbMatrix,list' dimnames(x) <- value # S4 method for class 'dbDataFrame' dimnames(x) # S4 method for class 'dbDataFrame,list' dimnames(x) <- value # S4 method for class 'dbMatrix,ANY' Arith(e1, e2) # S4 method for class 'ANY,dbMatrix' Arith(e1, e2) # S4 method for class 'dbMatrix,dbMatrix' Arith(e1, e2) # S4 method for class 'dbMatrix,ANY' Ops(e1, e2) # S4 method for class 'ANY,dbMatrix' Ops(e1, e2) # S4 method for class 'dbMatrix,dbMatrix' Ops(e1, e2) # S4 method for class 'dbDenseMatrix' rowSums(x, ...) # S4 method for class 'dbSparseMatrix' rowSums(x, ...) # S4 method for class 'dbDenseMatrix' colSums(x, ...) # S4 method for class 'dbSparseMatrix' colSums(x, ...) # S4 method for class 'dbDenseMatrix' rowMeans(x, ...) # S4 method for class 'dbSparseMatrix' rowMeans(x, ...) # S4 method for class 'dbDenseMatrix' colMeans(x, ...) # S4 method for class 'dbSparseMatrix' colMeans(x, ...) # S4 method for class 'dbDenseMatrix' colSds(x, ...) # S4 method for class 'dbSparseMatrix' colSds(x, ...) # S4 method for class 'dbDenseMatrix' rowSds(x, ...) # S4 method for class 'dbSparseMatrix' rowSds(x, ...) # S4 method for class 'dbDenseMatrix' mean(x, ...) # S4 method for class 'dbSparseMatrix' mean(x, ...) # S4 method for class 'dbMatrix' log(x, ...) # S4 method for class 'dbMatrix' t(x) # S4 method for class 'dbDataFrame' nrow(x) # S4 method for class 'dbMatrix' ncol(x) # S4 method for class 'dbDataFrame' ncol(x) # S4 method for class 'dbDataFrame' ncol(x) # S4 method for class 'dbMatrix' dim(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow.html","id":null,"dir":"Reference","previous_headings":"","what":"The number of rows/cols — nrow","title":"The number of rows/cols — nrow","text":"nrow ncol return number rows columns present x.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The number of rows/cols — nrow","text":"","code":"# S4 method for class 'dbMatrix' nrow(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":null,"dir":"Reference","previous_headings":"","what":"Precompute a dbMatrix table in a database — precompute","title":"Precompute a dbMatrix table in a database — precompute","text":"Precomputes dbMatrix table specificied database connection. can speed operations involve breaking sparsity dbSparseMatrix, cases performing + - arithmetic operations. Need run .","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Precompute a dbMatrix table in a database — precompute","text":"","code":"precompute(conn, m, n, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Precompute a dbMatrix table in a database — precompute","text":"conn duckdb database connection m number rows precomputed dbMatrix table n number columns precomputed dbMatrix table name name precomputed dbMatrix table created","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Precompute a dbMatrix table in a database — precompute","text":"num_rows num_cols parameters must exceed maximum row column indices dbMatrix order used densifying dbMatrix. params less maximum row column indices precomputed densification process fail. cases, run function larger n_rows num_cols, manually remove precomputed table set options(dbMatrix.precomp = NULL) R console.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Precompute a dbMatrix table in a database — precompute","text":"","code":"con = DBI::dbConnect(duckdb::duckdb(), \":memory:\") precompute(con = con , m = 100, n = 100, name = \"precomputed_table\") #> Precomputed dbMatrix 'precomputed_table' with #> 100 rows and 100 columns"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate array for pretty printing of matrix values — print_array","title":"Generate array for pretty printing of matrix values — print_array","text":"Generate array pretty printing matrix values","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate array for pretty printing of matrix values — print_array","text":"","code":"print_array( i = NULL, j = NULL, x = NULL, dims, rownames = rep(\"\", dims[1]), fill = \".\", digits = 5L )"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate array for pretty printing of matrix values — print_array","text":", j, x matched vectors integers j, value x dims dimensions array (integer vector 2) fill fill character digits default = 5. numeric, round number digits","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":null,"dir":"Reference","previous_headings":"","what":"read_MM — readMM","title":"read_MM — readMM","text":"Read matrix market file (.mtx .mtx.gz) database","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read_MM — readMM","text":"","code":"readMM(con, value, name = \"dbMatrix\", overwrite = FALSE, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_MM — readMM","text":"con DBI duckdb connection object (required) value path .mtx .mtx.gz file (required) name name assign file within database (optional). default: \"dbMatrix\" overwrite whether overwrite `name` already exists database. (required). default: FALSE ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read_MM — readMM","text":"tbl_dbi object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"read_MM — readMM","text":"Construct database VIEW .mtx .mtx.gz file columns '', 'j', 'x' representing row index, column index, value matrix, respectively. default '' 'j' type BIGINT 'x' type DOUBLE. Note: lack support R BIGINT may cause errors pulling data memory without proper type conversion. default, .mtx files expected contain two lines representing standard header information.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"read_MM — readMM","text":"","code":"print('TODO') #> [1] \"TODO\""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"read_matrix — read_matrix","title":"read_matrix — read_matrix","text":"Read tabular matrix files database","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read_matrix — read_matrix","text":"","code":"read_matrix(con, value, name = \"dbMatrix\", overwrite = FALSE, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_matrix — read_matrix","text":"con DBI duckdb connection object (required) value path .txt, .csv, .tsv .gzip/.gz variants (required) name name assign file within database (optional). default: \"dbMatrix\" overwrite whether overwrite `name` already exists database. (required). default: FALSE ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read_matrix — read_matrix","text":"tbl_dbi object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"read_matrix — read_matrix","text":"Construct database VIEW .csv, .tsv, .txt files .gz/.gzip variants","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"read_matrix — read_matrix","text":"","code":"print('TODO') #> [1] \"TODO\""},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute or save a dbMatrix to disk — save","title":"Compute or save a dbMatrix to disk — save","text":"Compute save dbMatrix disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute or save a dbMatrix to disk — save","text":"","code":"save(dbMatrix, name = \"\", overwrite = FALSE, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute or save a dbMatrix to disk — save","text":"dbMatrix dbMatrix object name name table save disk overwrite whether overwrite table already exists database ... additional params pass description Saves dbMatrix table specified name dbMatrix connection. Note: Computing persist database \":memory:\".","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Compute or save a dbMatrix to disk — save","text":"may break functions rely existing table. TODO: sync dbMatrix constructor compute","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compute or save a dbMatrix to disk — save","text":"","code":"dbm <- sim_dbSparseMatrix() #> Error in as(data, \"dgCMatrix\"): no method or default for coercing “matrix” to “dgCMatrix” compute(dbm, \"new_table\", overwrite = TRUE) #> Error in compute(dbm, \"new_table\", overwrite = TRUE): could not find function \"compute\""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":null,"dir":"Reference","previous_headings":"","what":"sim_dgc — sim_duckdb","title":"sim_dgc — sim_duckdb","text":"Simulate dbSparseMatrix memory Simulate dbDenseMatrix memory.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"sim_dgc — sim_duckdb","text":"","code":"sim_duckdb(value = datasets::iris, name = \"test\", con = NULL, memory = TRUE) sim_dgc(num_rows = 50, num_cols = 50, n_vals = 50) sim_denseMat(num_rows = 50, num_cols = 50) sim_ijx_matrix(mat_type = NULL, num_rows = 50, num_cols = 50, seed_num = 42) sim_dbDataFrame(value = NULL, name = \"df_test\", key = NA_character_) sim_dbSparseMatrix( num_rows = 50, num_cols = 50, seed_num = 42, name = \"sparse_test\", memory = FALSE ) sim_dbDenseMatrix( num_rows = 50, num_cols = 50, seed_num = 42, name = \"dense_test\", memory = FALSE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"sim_dgc — sim_duckdb","text":"num_rows number rows matrix (default: 50) num_cols number columns matrix (default: 50) seed_num seed number reproducibility (default: 42)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"sim_dgc — sim_duckdb","text":"dgCMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"sim_dgc — sim_duckdb","text":"function generates simulated sparse matrix (dgCMatrix) number rows columns sets n_vals random values non-zero value. function generates simulated dense matrix object specified number rows columns. function generates ijx representation simulated dgCMatrix object specified number rows columns sets 50 random values non-zero value.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"sim_dgc — sim_duckdb","text":"sim_duckdb(): Simulate duckdb connection dplyr tbl_Pool memory sim_dgc(): Simulate dgcMatrix sim_denseMat(): Simulate dense matrix sim_ijx_matrix(): Simulate duckdb connection dplyr tbl_Pool memory sim_dbDataFrame(): Simulate dbDataFrame memory sim_dbSparseMatrix(): Simulate dbSparseMatrix memory sim_dbDenseMatrix(): Simulate dbDenseMatrix memory","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"sim_dgc — sim_duckdb","text":"","code":"sim_ijx_matrix() #> Error in sim_ijx_matrix(): could not find function \"sim_ijx_matrix\""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbDataFrame-method.html","id":null,"dir":"Reference","previous_headings":"","what":"tail — tail,dbDataFrame-method","title":"tail — tail,dbDataFrame-method","text":"tail","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbDataFrame-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tail — tail,dbDataFrame-method","text":"","code":"# S4 method for class 'dbDataFrame' tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"tail — tail,dbMatrix-method","title":"tail — tail,dbMatrix-method","text":"tail","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tail — tail,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"Convert dbSparseMatrix dbDenseMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"","code":"toDbDense(db_sparse)"},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"db_sparse dbSparseMatrix object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"","code":"TODO #> Error in eval(expr, envir, enclos): object 'TODO' not found"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":null,"dir":"Reference","previous_headings":"","what":"to_ijx_disk — to_ijx_disk","title":"to_ijx_disk — to_ijx_disk","text":"to_ijx_disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"to_ijx_disk — to_ijx_disk","text":"","code":"to_ijx_disk(con, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"to_ijx_disk — to_ijx_disk","text":"con duckdb connection name name table convert ijx disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"to_ijx_disk — to_ijx_disk","text":"remote table long format unpivoted wide format matrix","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9021","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9021 (2024-07-05)","text":"Improve show function dbDenseMatrix. Updated simulate functions include overwrite param. Update .check_overwrite() internal function avoid bug overwritting passed table.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Add initial support reading .mtx files creating dbMatrix objects.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Update check_overwrite input validation","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Update Royxgen","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9019","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9019 (2024-03-18)","text":"Add new precompute function speed matrix densification. Add new show function dbDenseMatrix pretty color better spacing. Add new save function save dbMatrix. Add new input validation functions.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9019","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9019 (2024-03-18)","text":"Update docs. Update imports include glue, bit64 crayon.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Update constructor calls sim functions. Remove redundant con constructor. Remove db_path constructor. Constructor db_path arg change con object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Add dgTMatrix -memory matrix types supported dbMatrix constructor.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Set :memory: default db_path constructor. Update createDBMatrix docs.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"documentation-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Documentation","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Spacing. Update constructor fix. Remove :temp: place :memory:.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9017","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9017 (2024-02-07)","text":"Remove “:temp:” tests. Replace ‘:temp:’ ‘:memory:’. Add matrix addition dgCMatrix as_ijx().","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9017","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9017 (2024-02-07)","text":"Add unit tests scalar arith. Add unit tests names.R.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9017","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9017 (2024-02-07)","text":"Remove random browser() call. Add MatrixGenerics deps. Update gitignore.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9016","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9016 (2024-01-23)","text":"Add boolean indexing tests test-extract.R. Add as_ijx() convenience function. Update createDBMatrix() use dplyr::copy_to(). Update as_matrix() convenience function. Add unit tests extract methods.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9015","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9015 (2024-01-22)","text":"Add log(). Update toDbDense use dplyr instead SQL.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9015","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9015 (2024-01-22)","text":"Update DESCRIPTION include testthat. Update docs.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9014","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9014 (2024-01-19)","text":"update dbIndex superclass update as_matrix()","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Rename update dbIndex superclass fix indexing bugs.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Add experimental as_matrix() convenience function.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Update docs. Migrate site link drieslab. Move {Matrix} Imports.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"documentation-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Documentation","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Update overview.Rmd. Update operations vignette.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9012","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9012 (2023-12-08)","text":"densify necessary. != 0, +/-. toDbDense() previously updated table value. change update reference via VIEW creation table named ‘dense’.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9012","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9012 (2023-12-08)","text":"Add dbListTables().","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9012","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9012 (2023-12-08)","text":"Update docs. Update gitignore.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9011","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9011 (2023-12-08)","text":"Fix incorrect aggregate operations. Fixes con slot removal.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9011","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9011 (2023-12-08)","text":"Add get_con(). Add dbDisconnect() generic. Update accessors.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9011","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9011 (2023-12-08)","text":"Update vignettes. Update README. Update gitignore. Update docs. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://drieslab.github.io/dbMatrix/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. 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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"get-test-data","dir":"Articles","previous_headings":"","what":"Get test data","title":"Arithmetic","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object. file contains 634 rows 624 columns. rows represent gene names columns represent cell names. values integers represent number times gene detected cell. Like single-cell RNA-seq data, matrix sparse.","code":"dgc <- readRDS(\"../data/dgc.rds\") dplyr::glimpse(dgc) #> Loading required package: Matrix #> #> Attaching package: 'Matrix' #> The following object is masked from 'package:dbMatrix': #> #> readMM #> Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots #> ..@ i : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... #> ..@ p : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... #> ..@ Dim : int [1:2] 634 624 #> ..@ Dimnames:List of 2 #> .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... #> .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... #> ..@ x : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... #> ..@ factors : list()"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"create-a-dbmatrix-object","dir":"Articles","previous_headings":"","what":"Create a dbMatrix object","title":"Arithmetic","text":"Let’s create dbSparseMatrix object dgc object.","code":"# Note: by default the constructor creates a dbMatrix object in-memory con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\") dbsm <- createDBMatrix(value = dgc, con = con, name = 'visium', class = \"dbSparseMatrix\", overwrite = TRUE) # preview the object dbsm #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> #> Gna12 1 2 1 1 9 1 3 5 3 . #> Ccnd2 . 1 1 . . 1 . 1 1 . #> Btbd17 . 1 1 1 . . 2 . . . #> #> ......suppressing 614 columns and 628 rows #> #> Gm19935 . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"scalar-arithmetic","dir":"Articles","previous_headings":"","what":"Scalar Arithmetic","title":"Arithmetic","text":"dbMatrix emulates scalar arithmetic Matrix package. Note: Addition subtraction non-zero addends dbSparseMatrix results dbDenseMatrix.","code":"dbsm + 1 #> Warning in toDbDense(dbm): Densifying dbSparseMatrix on the fly. See #> ?precompute to speed up densification. #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbDenseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> 1 2 3 … 622 623 624 #> 1 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> 2 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> 3 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ #> 632 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> 633 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 #> 634 1e+00 1e+00 1e+00 … 1e+00 1e+00 1e+00 dbsm * 100 #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> #> Gna12 100 200 100 100 900 100 300 500 300 . #> Ccnd2 . 100 100 . . 100 . 100 100 . #> Btbd17 . 100 100 100 . . 200 . . . #> #> ......suppressing 614 columns and 628 rows #> #> Gm19935 . 100 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 100 . . . . . . . . 100"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-arithmetic","dir":"Articles","previous_headings":"","what":"Matrix Arithmetic","title":"Arithmetic","text":"dbMatrix also supports matrix arithmetic dbMatrix objects conformable.","code":"dbsm + dbsm #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> #> Gna12 2 4 2 2 18 2 6 10 6 . #> Ccnd2 . 2 2 . . 2 . 2 2 . #> Btbd17 . 2 2 2 . . 4 . . . #> #> ......suppressing 614 columns and 628 rows #> #> Gm19935 . 2 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 2 . . . . . . . . 2"},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"hadamard-product","dir":"Articles","previous_headings":"Matrix Multiplication","what":"Hadamard product","title":"Arithmetic","text":"","code":"dbsm * dbsm #> connection : :memory: #> table name : 'visium' #> 634 x 624 matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #> #> Gna12 1 4 1 1 81 1 9 25 9 . #> Ccnd2 . 1 1 . . 1 . 1 1 . #> Btbd17 . 1 1 1 . . 4 . . . #> #> ......suppressing 614 columns and 628 rows #> #> Gm19935 . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-product","dir":"Articles","previous_headings":"Matrix Multiplication","what":"Matrix product","title":"Arithmetic","text":"TODO","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"shutdown","dir":"Articles","previous_headings":"","what":"Shutdown","title":"Arithmetic","text":"","code":"dbMatrix::dbDisconnect(dbsm, shutdown = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Arithmetic","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #> #> Matrix products: default #> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 #> #> locale: #> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 #> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 #> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C #> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C #> #> time zone: UTC #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] Matrix_1.7-0 dbMatrix_0.0.0.9021 MatrixGenerics_1.16.0 #> [4] matrixStats_1.3.0 #> #> loaded via a namespace (and not attached): #> [1] bit_4.0.5 jsonlite_1.8.8 crayon_1.5.3 dplyr_1.1.4 #> [5] compiler_4.4.1 tidyselect_1.2.1 blob_1.2.4 jquerylib_0.1.4 #> [9] systemfonts_1.1.0 textshaping_0.4.0 yaml_2.3.9 fastmap_1.2.0 #> [13] lattice_0.22-6 R6_2.5.1 generics_0.1.3 knitr_1.48 #> [17] tibble_3.2.1 desc_1.4.3 DBI_1.2.3 bslib_0.7.0 #> [21] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 cachem_1.1.0 #> [25] xfun_0.45 fs_1.6.4 sass_0.4.9 bit64_4.0.5 #> [29] cli_3.6.3 withr_3.0.0 pkgdown_2.1.0 magrittr_2.0.3 #> [33] digest_0.6.36 grid_4.4.1 dbplyr_2.5.0 lifecycle_1.0.4 #> [37] vctrs_0.6.5 evaluate_0.24.0 glue_1.7.0 data.table_1.15.4 #> [41] duckdb_1.0.0-1 ragg_1.3.2 fansi_1.0.6 purrr_1.0.2 #> [45] rmarkdown_2.27 tools_4.4.1 pkgconfig_2.0.3 htmltools_0.5.8.1"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Operations","text":"vignette introduces generic functions operations supported dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"loading-library","dir":"Articles","previous_headings":"","what":"Loading library","title":"Operations","text":"","code":"library(dbMatrix) library(Matrix)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbmatrix-generics","dir":"Articles","previous_headings":"","what":"dbMatrix generics","title":"Operations","text":"dbMatrix subclasses currently support basic generic functions listed support operations coming soon.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"get-test-data","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Get test data","title":"Operations","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object.","code":"dgc <- readRDS(\"../data/dgc.rds\") dplyr::glimpse(dgc) ## Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots ## ..@ i : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... ## ..@ p : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... ## ..@ Dim : int [1:2] 634 624 ## ..@ Dimnames:List of 2 ## .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... ## .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... ## ..@ x : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... ## ..@ factors : list() # create dbSparseMatrix from the same dgc con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\") sparse <- createDBMatrix(value = dgc, con = con, name = 'visium', class = \"dbSparseMatrix\", overwrite = TRUE) # preview # show function aims to emulate the show method for dgCMatrix head(sparse) ## connection : :memory: ## table name : 'visium' ## 6 x 624 matrix of class \"dbSparseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ## ## Gna12 1 2 1 1 9 1 3 5 3 . ## [ reached getOption(\"max.print\") -- omitted 633 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(sparse) ## connection : :memory: ## table name : 'visium' ## 624 x 634 matrix of class \"dbSparseMatrix\" ## [[ Colnames 'Gna12', 'Ccnd2', 'Btbd17' ... suppressing 628 ...'Gm19935', '9630013A20Rik', '2900040C04Rik' ]] ## ## AAAGGGATGTAGCAAG-1 1 . . . . . 1 . . . ## [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ## ## ......suppressing 624 columns and 618 rows ## ## NA ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(sparse) ## AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1 ## 0.7413249 1.3296530 1.1435331 0.8343849 ## AACAACTGGTAGTTGC-1 AACAGGAAATCGAATA-1 AACAGGATGGGCCGCG-1 AACCATGGGATCGCTA-1 ## 1.6135647 2.2129338 1.7223975 1.9022082 ## AACCCAGAGACGGAGA-1 AACCGAGCTTGGTCAT-1 ## 0.7397476 0.9258675 ## [ reached getOption(\"max.print\") -- omitted 614 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(sparse) ## AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1 ## 470 843 725 529 ## AACAACTGGTAGTTGC-1 AACAGGAAATCGAATA-1 AACAGGATGGGCCGCG-1 AACCATGGGATCGCTA-1 ## 1023 1403 1092 1206 ## AACCCAGAGACGGAGA-1 AACCGAGCTTGGTCAT-1 ## 469 587 ## [ reached getOption(\"max.print\") -- omitted 614 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(sparse) ## Gna12 Ccnd2 Btbd17 Sox9 Sez6 Serpinf1 S100a6 Col1a1 ## 2.7179487 1.7323718 0.5528846 0.8766026 4.4679487 0.3092949 1.6522436 0.1185897 ## Vwf Esam ## 0.6346154 0.4391026 ## [ reached getOption(\"max.print\") -- omitted 624 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(sparse) ## Gna12 Ccnd2 Btbd17 Sox9 Sez6 Serpinf1 S100a6 Col1a1 ## 1696 1081 345 547 2788 193 1031 74 ## Vwf Esam ## 396 274 ## [ reached getOption(\"max.print\") -- omitted 624 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"dim","title":"Operations","text":"","code":"dim(sparse) ## [1] 634 624 dim(dgc) ## [1] 634 624"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"check-results-are-equivalent","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Check results are equivalent","title":"Operations","text":"","code":"all.equal(dbMatrix::colMeans(sparse), Matrix::colMeans(dgc)) ## [1] TRUE all.equal(dbMatrix::colSums(sparse), Matrix::colSums(dgc)) ## [1] TRUE all.equal(dbMatrix::rowMeans(sparse), Matrix::rowMeans(dgc)) ## [1] TRUE all.equal(dbMatrix::rowSums(sparse), Matrix::rowSums(dgc)) ## [1] TRUE"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbdensematrix-operations","dir":"Articles","previous_headings":"","what":"dbDenseMatrix Operations","title":"Operations","text":"","code":"# below is a convenience function to simulate a dbDenseMatrix dense = dbMatrix::sim_dbDenseMatrix() # preview dense ## connection : /tmp/RtmpNLoJMo/file180317474a4a.duckdb ## table name : 'dense_test' ## 50 x 50 matrix of class \"dbDenseMatrix\" ## 1 2 3 … 48 49 50 ## 1 1.4e+00 3.2e-01 1.2e+00 … 2.2e-01 1.3e+00 -3.9e-01 ## 2 -5.6e-01 -7.8e-01 1.0e+00 … -1.1e-01 -6.0e-01 -9.9e-02 ## 3 3.6e-01 1.6e+00 -1.0e+00 … 2.0e-02 5.7e-02 -2.8e-02 ## ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ## 48 1.4e+00 -1.5e+00 -4.3e-01 … -7.4e-02 -3.5e-02 7.0e-01 ## 49 -4.3e-01 8.0e-02 7.0e-01 … -7.7e-01 -9.2e-01 -1.4e-01 ## 50 6.6e-01 6.5e-01 -1.1e+00 … 5.9e-01 1.1e+00 5.0e-01"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(dense) ## connection : /tmp/RtmpNLoJMo/file180317474a4a.duckdb ## table name : 'dense_test' ## 50 x 50 matrix of class \"dbDenseMatrix\" ## [[ Colnames 'row1', 'row2', 'row3' ... suppressing 44 ...'row48', 'row49', 'row50' ]] ## 1 2 3 … 48 49 50 ## 1 1.4e+00 -5.6e-01 3.6e-01 … 1.4e+00 -4.3e-01 6.6e-01 ## 2 3.2e-01 -7.8e-01 1.6e+00 … -1.5e+00 8.0e-02 6.5e-01 ## 3 1.2e+00 1.0e+00 -1.0e+00 … -4.3e-01 7.0e-01 -1.1e+00 ## ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ## 48 2.2e-01 -1.1e-01 2.0e-02 … -7.4e-02 -7.7e-01 5.9e-01 ## 49 1.3e+00 -6.0e-01 5.7e-02 … -3.5e-02 -9.2e-01 1.1e+00 ## 50 -3.9e-01 -9.9e-02 -2.8e-02 … 7.0e-01 -1.4e-01 5.0e-01"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(dense) ## col1 col2 col3 col4 col5 col6 ## -0.035671782 0.100701413 -0.151251089 -0.023716326 0.007939877 -0.028676220 ## col7 col8 col9 col10 ## -0.061541347 0.127414276 -0.119421148 -0.116239863 ## [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(dense) ## col1 col2 col3 col4 col5 col6 col7 ## -1.7835891 5.0350707 -7.5625544 -1.1858163 0.3969938 -1.4338110 -3.0770674 ## col8 col9 col10 ## 6.3707138 -5.9710574 -5.8119931 ## [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(dense) ## row1 row2 row3 row4 row5 row6 ## 0.053643638 0.002494642 0.031334034 0.093889009 -0.048311439 -0.047287825 ## row7 row8 row9 row10 ## 0.092209664 -0.023069981 0.096433464 -0.093495713 ## [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(dense) ## row1 row2 row3 row4 row5 row6 row7 ## 2.6821819 0.1247321 1.5667017 4.6944505 -2.4155720 -2.3643912 4.6104832 ## row8 row9 row10 ## -1.1534990 4.8216732 -4.6747857 ## [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"mean","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"mean","title":"Operations","text":"","code":"dbMatrix::mean(dense) ## [1] -0.009673541"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"dim","title":"Operations","text":"","code":"dim(dense) ## [1] 50 50"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"shutdown","dir":"Articles","previous_headings":"","what":"Shutdown","title":"Operations","text":"","code":"dbMatrix::dbDisconnect(dense, shutdown = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Operations","text":"","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## ## Matrix products: default ## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 ## ## locale: ## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 ## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 ## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C ## [10] LC_TELEPHONE=C ## [ reached getOption(\"max.print\") -- omitted 2 entries ] ## ## time zone: UTC ## tzcode source: system (glibc) ## ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: ## [1] Matrix_1.7-0 dbMatrix_0.0.0.9021 MatrixGenerics_1.16.0 ## [4] matrixStats_1.3.0 ## ## loaded via a namespace (and not attached): ## [1] jsonlite_1.8.8 crayon_1.5.3 dplyr_1.1.4 compiler_4.4.1 ## [5] tidyselect_1.2.1 blob_1.2.4 jquerylib_0.1.4 systemfonts_1.1.0 ## [9] textshaping_0.4.0 yaml_2.3.9 ## [ reached getOption(\"max.print\") -- omitted 36 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbmatrix","dir":"Articles","previous_headings":"","what":"dbMatrix","title":"Overview","text":"dbMatrix core package dbverse library inherits dbData base class consists two subclasses, dbSparseMatrix dbDenseMatrix. dbMatrix objects emulate -memory dense sparse matrices embedded database powered DuckDB.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbsparsematrix","dir":"Articles","previous_headings":"","what":"dbSparseMatrix","title":"Overview","text":"Sparse matrices represented triplet vectors , j, x numerical vectors. j refer row column indices, respectively, specific x values counts. Note: j vectors one-based following conventions Matrix R package TSparseMatrix class. dbSparseMatrix class stores triplet vector representation associated dimension names dimensions available. none provided, automatically generated factors (enums) row# col# labels rownames colnames, respectively. dbSparseMatrix class contain zeros triplet vector representation. Zero values inferred based provided dimensions. Support compressed sparse column matrices dgCMatrix class Matrix R package currently implemented. information sparse matrices, see wiki article .","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbdensematrix","dir":"Articles","previous_headings":"","what":"dbDenseMatrix","title":"Overview","text":"use approach dbSparseMatrix represent dense matrix triplet , j, x vector. difference dbDenseMatrix class consists values matrix, including zeros.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edward C. Ruiz. Author. Jiaji George Chen. Author. Ruben Dries. Author, maintainer.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"C. Ruiz E, George Chen J, Dries R (2024). dbMatrix: dbMatrix. R package version 0.0.0.9021, https://drieslab.github.io/dbMatrix/.","code":"@Manual{, title = {dbMatrix: dbMatrix}, author = {Edward {C. Ruiz} and Jiaji {George Chen} and Ruben Dries}, year = {2024}, note = {R package version 0.0.0.9021}, url = {https://drieslab.github.io/dbMatrix/}, }"},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"dbmatrix","dir":"","previous_headings":"","what":"dbMatrix","title":"dbMatrix","text":"dbMatrix core package dbverse library. goal dbMatrix support larger--memory matrix computations.","code":""},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"dbMatrix","text":"can install development version dbMatrix Github like :","code":"# install.packages(\"pak\", repos = sprintf(\"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch)) pak::pak(\"drieslab/dbMatrix\")"},{"path":"https://drieslab.github.io/dbMatrix/reference/DBI.html","id":null,"dir":"Reference","previous_headings":"","what":"dbDisconnect — dbDisconnect,dbMatrix-method","title":"dbDisconnect — dbDisconnect,dbMatrix-method","text":"dbDisconnect dbListTables","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/DBI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dbDisconnect — dbDisconnect,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' dbDisconnect(x, ...) # S4 method for class 'dbMatrix' dbListTables(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":null,"dir":"Reference","previous_headings":"","what":"Set a column to numeric — castNumeric","title":"Set a column to numeric — castNumeric","text":"Sets column numeric first checking column data type. nothing column already double precaution avoid truncation values.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set a column to numeric — castNumeric","text":"","code":"# S4 method for class 'dbData,character' castNumeric(x, col, ...) # S4 method for class 'dbMatrix,missing' castNumeric(x, col, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set a column to numeric — castNumeric","text":"x dbData data object col column cast numeric ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Column data types of dbData objects — colTypes","title":"Column data types of dbData objects — colTypes","text":"Get column data types objects inherit 'dbData'","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Column data types of dbData objects — colTypes","text":"","code":"# S4 method for class 'dbData' colTypes(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Column data types of dbData objects — colTypes","text":"x dbData data object ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a sparse or dense dbMatrix object — createDBMatrix","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"Create S4 dbMatrix object sparse dense triplet vector format.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"","code":"createDBMatrix( value, class = NULL, con = NULL, overwrite = FALSE, name = \"dbMatrix\", dims = NULL, dim_names = NULL, mtx_rowname_file_path, mtx_rowname_col_idx = 1, mtx_colname_file_path, mtx_colname_col_idx = 1, ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"value data added database. See details supported data types (required) class class dbMatrix: dbDenseMatrix dbSparseMatrix (required) con DBI duckdb connection object (required) overwrite whether overwrite table already exists database (required) name table name assign within database (optional, default: \"dbMatrix\") dims dimensions matrix (optional: [int, int]) dim_names dimension names matrix (optional: list(enum, enum)) mtx_rowname_file_path path .mtx rowname file read (optional) database. default, header assumed. mtx_rowname_col_idx column index row name file (optional) mtx_colname_file_path path .mtx colname file read database. default, header assumed. (optional) mtx_colname_col_idx column index column name file (optional) ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"function reads data pre-existing DuckDB database. Based name db_path lazy connection made downstream dbMatrix initialization. Supported value data types: dgCMatrix -memory sparse matrix Matrix package dgTMatrix -memory triplet vector COO matrix matrix -memory dense matrix base R .mtx Path .mtx file (TODO) .csv Path .csv file (TODO) tbl_duckdb_connection Table DuckDB database ijx format existing dbMatrix object. dims dim_names must specified value tbl_duckdb_connection.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"","code":"dgc <- dbMatrix:::sim_dgc() #> Error in as(data, \"dgCMatrix\"): no method or default for coercing “matrix” to “dgCMatrix” dbSparse <- createDBMatrix(value = dgc, db_path = \":memory:\", name = \"sparse_matrix\", class = \"dbSparseMatrix\", overwrite = TRUE) #> Error in eval(expr, envir, enclos): object 'dgc' not found dbSparse #> Error in eval(expr, envir, enclos): object 'dbSparse' not found"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDataFrame-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dbDataFrame class — dbDataFrame-class","title":"S4 dbDataFrame class — dbDataFrame-class","text":"Representation dataframes using -disk database. object used connection single table exists within database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDataFrame-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dbDataFrame class — dbDataFrame-class","text":"data dplyr tbl represents database data hash unique hash ID backend remote_name name table within database contains data key column set key ordering subsetting ","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDenseMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","title":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","text":"Representation dense matrices using -disk database. Inherits dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDenseMatrix-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","text":"data dense ijx dataframe/tibble","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dbMatrix class — dbMatrix-class","title":"S4 dbMatrix class — dbMatrix-class","text":"Representation sparse matrices using -disk database. object used connection single table exists within database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dbMatrix class — dbMatrix-class","text":"dim_names row [1] col [2] names dims dimensions matrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbSparseMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 Class for dbSparseMatrix — dbSparseMatrix-class","title":"S4 Class for dbSparseMatrix — dbSparseMatrix-class","text":"Representation sparse matrices using -disk database. Inherits dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for conn arg — .check_con","title":"Input validation for conn arg — .check_con","text":"Input validation conn arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for conn arg — .check_con","text":"","code":".check_con(conn)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Input validation for conn arg — .check_con","text":"conn tbl_duckdb_connection object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for name arg — .check_name","title":"Input validation for name arg — .check_name","text":"Input validation name arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for name arg — .check_name","text":"","code":".check_name(name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_overwrite.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for overwrite arg — .check_overwrite","title":"Input validation for overwrite arg — .check_overwrite","text":"Input validation overwrite arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_overwrite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for overwrite arg — .check_overwrite","text":"","code":".check_overwrite(conn, overwrite, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for data arg — .check_value","title":"Input validation for data arg — .check_value","text":"Input validation data arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for data arg — .check_value","text":"","code":".check_value(value)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Input validation for data arg — .check_value","text":"x Matrix, matrix, tbl_duckdb_connection object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":null,"dir":"Reference","previous_headings":"","what":"flex_window_order — flex_window_order","title":"flex_window_order — flex_window_order","text":"workaround multiple dbplyr window column ordering","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"flex_window_order — flex_window_order","text":"","code":"flex_window_order(x, order_cols)"},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"flex_window_order — flex_window_order","text":"x dbplyr::tbl_lazy order_cols character vector column names","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":null,"dir":"Reference","previous_headings":"","what":"get_MM_dim — get_MM_dim","title":"get_MM_dim — get_MM_dim","text":"Internal function read dimensions .mtx file","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_MM_dim — get_MM_dim","text":"","code":"get_MM_dim(mtx_file_path)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_MM_dim — get_MM_dim","text":"mtx_file_path path .mtx file read database","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_MM_dim — get_MM_dim","text":"integer vector dimensions","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"get_MM_dim — get_MM_dim","text":"Scans header mtx file (starting representing dimensions number nonzero values. Note: header size can vary depending .mtx file.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":null,"dir":"Reference","previous_headings":"","what":"get_MM_dimnames — get_MM_dimnames","title":"get_MM_dimnames — get_MM_dimnames","text":"Internal function read row column names .mtx file","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_MM_dimnames — get_MM_dimnames","text":"","code":"get_MM_dimnames( mtx_file_path, mtx_rowname_file_path, mtx_rowname_col_idx = 1, mtx_colname_file_path, mtx_colname_col_idx = 1, ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_MM_dimnames — get_MM_dimnames","text":"mtx_file_path path .mtx file read database mtx_rowname_file_path path .mtx rowname file read database. default, header assumed. mtx_rowname_col_idx column index row name file mtx_colname_file_path path .mtx colname file read database. default, header assumed. mtx_colname_col_idx column index column name file ... additional params pass data.table::fread","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_MM_dimnames — get_MM_dimnames","text":"list row column name character vectors","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"get_MM_dimnames — get_MM_dimnames","text":"Can used read row column names .mtx files. Note: files must contain header (colnames). mtx_rowname_col_idx mtx_colname_col_idx can used specify column index row column name files, respectively. default, first column used . TODO: Support reading rownames colnames.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":null,"dir":"Reference","previous_headings":"","what":"get_con — get_con","title":"get_con — get_con","text":"get_con","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_con — get_con","text":"","code":"get_con(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_con — get_con","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":null,"dir":"Reference","previous_headings":"","what":"get_dbdir — get_dbdir","title":"get_dbdir — get_dbdir","text":"get_dbdir","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_dbdir — get_dbdir","text":"","code":"get_dbdir(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_dbdir — get_dbdir","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":null,"dir":"Reference","previous_headings":"","what":"get_tblName — get_tblName","title":"get_tblName — get_tblName","text":"get_tblName","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_tblName — get_tblName","text":"","code":"get_tblName(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_tblName — get_tblName","text":"dbData","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbDataFrame-method.html","id":null,"dir":"Reference","previous_headings":"","what":"head — head,dbDataFrame-method","title":"head — head,dbDataFrame-method","text":"head","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbDataFrame-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"head — head,dbDataFrame-method","text":"","code":"# S4 method for class 'dbDataFrame' head(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"head — head,dbMatrix-method","title":"head — head,dbMatrix-method","text":"head","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"head — head,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' head(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/hidden_aliases.html","id":null,"dir":"Reference","previous_headings":"","what":"rowSums — [,dbData,missing,missing,missing-method","title":"rowSums — [,dbData,missing,missing,missing-method","text":"rowSums rowSums colSums colSums rowMeans rowMeans colMeans colMeans colSds colSds rowSds rowSds mean mean log Transpose nrow ncol ncol ncol dim","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/hidden_aliases.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rowSums — [,dbData,missing,missing,missing-method","text":"","code":"# S4 method for class 'dbData,missing,missing,missing' x[i, j] # S4 method for class 'dbData,missing,missing,ANY' x[i, j] <- value # S4 method for class 'dbMatrix,dbIndex,missing,missing' x[i, j, ..., drop = TRUE] # S4 method for class 'dbMatrix,missing,dbIndex,missing' x[i, j, ..., drop = TRUE] # S4 method for class 'dbMatrix,dbIndex,dbIndex,missing' x[i, j, ..., drop = TRUE] # S4 method for class 'dbDataFrame,dbIndex,missing,ANY' x[i, j, ..., drop = TRUE] # S4 method for class 'dbDataFrame,missing,dbIndex,ANY' x[i, j, ..., drop = TRUE] # S4 method for class 'dbDataFrame,dbIndex,dbIndex,ANY' x[i, j, ..., drop = FALSE] # S4 method for class 'dbDataFrame,missing,missing,missing' x[i, j] # S4 method for class 'dbDataFrame,missing,missing,ANY' x[i, j] <- value # S4 method for class 'dbDataFrame' names(x) # S4 method for class 'dbDataFrame,dbIndex' names(x) <- value # S4 method for class 'dbData' rownames(x) # S4 method for class 'dbMatrix' rownames(x) # S4 method for class 'dbMatrix' rownames(x) <- value # S4 method for class 'dbData' colnames(x) # S4 method for class 'dbMatrix' colnames(x) # S4 method for class 'dbMatrix,ANY' colnames(x) <- value # S4 method for class 'dbDataFrame,dbIndex' colnames(x) <- value # S4 method for class 'dbMatrix' dimnames(x) # S4 method for class 'dbMatrix,list' dimnames(x) <- value # S4 method for class 'dbDataFrame' dimnames(x) # S4 method for class 'dbDataFrame,list' dimnames(x) <- value # S4 method for class 'dbMatrix,ANY' Arith(e1, e2) # S4 method for class 'ANY,dbMatrix' Arith(e1, e2) # S4 method for class 'dbMatrix,dbMatrix' Arith(e1, e2) # S4 method for class 'dbMatrix,ANY' Ops(e1, e2) # S4 method for class 'ANY,dbMatrix' Ops(e1, e2) # S4 method for class 'dbMatrix,dbMatrix' Ops(e1, e2) # S4 method for class 'dbDenseMatrix' rowSums(x, ...) # S4 method for class 'dbSparseMatrix' rowSums(x, ...) # S4 method for class 'dbDenseMatrix' colSums(x, ...) # S4 method for class 'dbSparseMatrix' colSums(x, ...) # S4 method for class 'dbDenseMatrix' rowMeans(x, ...) # S4 method for class 'dbSparseMatrix' rowMeans(x, ...) # S4 method for class 'dbDenseMatrix' colMeans(x, ...) # S4 method for class 'dbSparseMatrix' colMeans(x, ...) # S4 method for class 'dbDenseMatrix' colSds(x, ...) # S4 method for class 'dbSparseMatrix' colSds(x, ...) # S4 method for class 'dbDenseMatrix' rowSds(x, ...) # S4 method for class 'dbSparseMatrix' rowSds(x, ...) # S4 method for class 'dbDenseMatrix' mean(x, ...) # S4 method for class 'dbSparseMatrix' mean(x, ...) # S4 method for class 'dbMatrix' log(x, ...) # S4 method for class 'dbMatrix' t(x) # S4 method for class 'dbDataFrame' nrow(x) # S4 method for class 'dbMatrix' ncol(x) # S4 method for class 'dbDataFrame' ncol(x) # S4 method for class 'dbDataFrame' ncol(x) # S4 method for class 'dbMatrix' dim(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow.html","id":null,"dir":"Reference","previous_headings":"","what":"The number of rows/cols — nrow","title":"The number of rows/cols — nrow","text":"nrow ncol return number rows columns present x.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The number of rows/cols — nrow","text":"","code":"# S4 method for class 'dbMatrix' nrow(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":null,"dir":"Reference","previous_headings":"","what":"Precompute a dbMatrix table in a database — precompute","title":"Precompute a dbMatrix table in a database — precompute","text":"Precomputes dbMatrix table specificied database connection. can speed operations involve breaking sparsity dbSparseMatrix, cases performing + - arithmetic operations. Need run .","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Precompute a dbMatrix table in a database — precompute","text":"","code":"precompute(conn, m, n, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Precompute a dbMatrix table in a database — precompute","text":"conn duckdb database connection m number rows precomputed dbMatrix table n number columns precomputed dbMatrix table name name precomputed dbMatrix table created","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Precompute a dbMatrix table in a database — precompute","text":"num_rows num_cols parameters must exceed maximum row column indices dbMatrix order used densifying dbMatrix. params less maximum row column indices precomputed densification process fail. cases, run function larger n_rows num_cols, manually remove precomputed table set options(dbMatrix.precomp = NULL) R console.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Precompute a dbMatrix table in a database — precompute","text":"","code":"con = DBI::dbConnect(duckdb::duckdb(), \":memory:\") precompute(con = con , m = 100, n = 100, name = \"precomputed_table\") #> Precomputed dbMatrix 'precomputed_table' with #> 100 rows and 100 columns"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate array for pretty printing of matrix values — print_array","title":"Generate array for pretty printing of matrix values — print_array","text":"Generate array pretty printing matrix values","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate array for pretty printing of matrix values — print_array","text":"","code":"print_array( i = NULL, j = NULL, x = NULL, dims, rownames = rep(\"\", dims[1]), fill = \".\", digits = 5L )"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate array for pretty printing of matrix values — print_array","text":", j, x matched vectors integers j, value x dims dimensions array (integer vector 2) fill fill character digits default = 5. numeric, round number digits","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":null,"dir":"Reference","previous_headings":"","what":"read_MM — readMM","title":"read_MM — readMM","text":"Read matrix market file (.mtx .mtx.gz) database","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read_MM — readMM","text":"","code":"readMM(con, value, name = \"dbMatrix\", overwrite = FALSE, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_MM — readMM","text":"con DBI duckdb connection object (required) value path .mtx .mtx.gz file (required) name name assign file within database (optional). default: \"dbMatrix\" overwrite whether overwrite `name` already exists database. (required). default: FALSE ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read_MM — readMM","text":"tbl_dbi object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"read_MM — readMM","text":"Construct database VIEW .mtx .mtx.gz file columns '', 'j', 'x' representing row index, column index, value matrix, respectively. default '' 'j' type BIGINT 'x' type DOUBLE. Note: lack support R BIGINT may cause errors pulling data memory without proper type conversion. default, .mtx files expected contain two lines representing standard header information.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/readMM.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"read_MM — readMM","text":"","code":"print('TODO') #> [1] \"TODO\""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"read_matrix — read_matrix","title":"read_matrix — read_matrix","text":"Read tabular matrix files database","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read_matrix — read_matrix","text":"","code":"read_matrix(con, value, name = \"dbMatrix\", overwrite = FALSE, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_matrix — read_matrix","text":"con DBI duckdb connection object (required) value path .txt, .csv, .tsv .gzip/.gz variants (required) name name assign file within database (optional). default: \"dbMatrix\" overwrite whether overwrite `name` already exists database. (required). default: FALSE ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read_matrix — read_matrix","text":"tbl_dbi object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"read_matrix — read_matrix","text":"Construct database VIEW .csv, .tsv, .txt files .gz/.gzip variants","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/read_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"read_matrix — read_matrix","text":"","code":"print('TODO') #> [1] \"TODO\""},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute or save a dbMatrix to disk — save","title":"Compute or save a dbMatrix to disk — save","text":"Compute save dbMatrix disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute or save a dbMatrix to disk — save","text":"","code":"save(dbMatrix, name = \"\", overwrite = FALSE, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute or save a dbMatrix to disk — save","text":"dbMatrix dbMatrix object name name table save disk overwrite whether overwrite table already exists database ... additional params pass description Saves dbMatrix table specified name dbMatrix connection. Note: Computing persist database \":memory:\".","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Compute or save a dbMatrix to disk — save","text":"may break functions rely existing table. TODO: sync dbMatrix constructor compute","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/save.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compute or save a dbMatrix to disk — save","text":"","code":"dbm <- sim_dbSparseMatrix() #> Error in as(data, \"dgCMatrix\"): no method or default for coercing “matrix” to “dgCMatrix” compute(dbm, \"new_table\", overwrite = TRUE) #> Error in compute(dbm, \"new_table\", overwrite = TRUE): could not find function \"compute\""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":null,"dir":"Reference","previous_headings":"","what":"sim_dgc — sim_duckdb","title":"sim_dgc — sim_duckdb","text":"Simulate dbSparseMatrix memory Simulate dbDenseMatrix memory.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"sim_dgc — sim_duckdb","text":"","code":"sim_duckdb(value = datasets::iris, name = \"test\", con = NULL, memory = TRUE) sim_dgc(num_rows = 50, num_cols = 50, n_vals = 50) sim_denseMat(num_rows = 50, num_cols = 50) sim_ijx_matrix(mat_type = NULL, num_rows = 50, num_cols = 50, seed_num = 42) sim_dbDataFrame(value = NULL, name = \"df_test\", key = NA_character_) sim_dbSparseMatrix( num_rows = 50, num_cols = 50, seed_num = 42, name = \"sparse_test\", memory = FALSE ) sim_dbDenseMatrix( num_rows = 50, num_cols = 50, seed_num = 42, name = \"dense_test\", memory = FALSE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"sim_dgc — sim_duckdb","text":"num_rows number rows matrix (default: 50) num_cols number columns matrix (default: 50) seed_num seed number reproducibility (default: 42)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"sim_dgc — sim_duckdb","text":"dgCMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"sim_dgc — sim_duckdb","text":"function generates simulated sparse matrix (dgCMatrix) number rows columns sets n_vals random values non-zero value. function generates simulated dense matrix object specified number rows columns. function generates ijx representation simulated dgCMatrix object specified number rows columns sets 50 random values non-zero value.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"sim_dgc — sim_duckdb","text":"sim_duckdb(): Simulate duckdb connection dplyr tbl_Pool memory sim_dgc(): Simulate dgcMatrix sim_denseMat(): Simulate dense matrix sim_ijx_matrix(): Simulate duckdb connection dplyr tbl_Pool memory sim_dbDataFrame(): Simulate dbDataFrame memory sim_dbSparseMatrix(): Simulate dbSparseMatrix memory sim_dbDenseMatrix(): Simulate dbDenseMatrix memory","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"sim_dgc — sim_duckdb","text":"","code":"sim_ijx_matrix() #> Error in sim_ijx_matrix(): could not find function \"sim_ijx_matrix\""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbDataFrame-method.html","id":null,"dir":"Reference","previous_headings":"","what":"tail — tail,dbDataFrame-method","title":"tail — tail,dbDataFrame-method","text":"tail","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbDataFrame-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tail — tail,dbDataFrame-method","text":"","code":"# S4 method for class 'dbDataFrame' tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"tail — tail,dbMatrix-method","title":"tail — tail,dbMatrix-method","text":"tail","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tail — tail,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"Convert dbSparseMatrix dbDenseMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"","code":"toDbDense(db_sparse)"},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"db_sparse dbSparseMatrix object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"","code":"TODO #> Error in eval(expr, envir, enclos): object 'TODO' not found"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":null,"dir":"Reference","previous_headings":"","what":"to_ijx_disk — to_ijx_disk","title":"to_ijx_disk — to_ijx_disk","text":"to_ijx_disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"to_ijx_disk — to_ijx_disk","text":"","code":"to_ijx_disk(con, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"to_ijx_disk — to_ijx_disk","text":"con duckdb connection name name table convert ijx disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"to_ijx_disk — to_ijx_disk","text":"remote table long format unpivoted wide format matrix","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9021","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9021 (2024-07-05)","text":"Improve show function dbDenseMatrix. Updated simulate functions include overwrite param. Update .check_overwrite() internal function avoid bug overwritting passed table.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Add initial support reading .mtx files creating dbMatrix objects.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Update check_overwrite input validation","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Update Royxgen","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9019","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9019 (2024-03-18)","text":"Add new precompute function speed matrix densification. Add new show function dbDenseMatrix pretty color better spacing. Add new save function save dbMatrix. Add new input validation functions.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9019","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9019 (2024-03-18)","text":"Update docs. Update imports include glue, bit64 crayon.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Update constructor calls sim functions. Remove redundant con constructor. Remove db_path constructor. Constructor db_path arg change con object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Add dgTMatrix -memory matrix types supported dbMatrix constructor.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Set :memory: default db_path constructor. Update createDBMatrix docs.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"documentation-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Documentation","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Spacing. Update constructor fix. Remove :temp: place :memory:.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9017","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9017 (2024-02-07)","text":"Remove “:temp:” tests. Replace ‘:temp:’ ‘:memory:’. Add matrix addition dgCMatrix as_ijx().","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9017","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9017 (2024-02-07)","text":"Add unit tests scalar arith. Add unit tests names.R.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9017","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9017 (2024-02-07)","text":"Remove random browser() call. Add MatrixGenerics deps. Update gitignore.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9016","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9016 (2024-01-23)","text":"Add boolean indexing tests test-extract.R. Add as_ijx() convenience function. Update createDBMatrix() use dplyr::copy_to(). Update as_matrix() convenience function. Add unit tests extract methods.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9015","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9015 (2024-01-22)","text":"Add log(). Update toDbDense use dplyr instead SQL.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9015","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9015 (2024-01-22)","text":"Update DESCRIPTION include testthat. Update docs.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9014","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9014 (2024-01-19)","text":"update dbIndex superclass update as_matrix()","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Rename update dbIndex superclass fix indexing bugs.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Add experimental as_matrix() convenience function.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Update docs. Migrate site link drieslab. Move {Matrix} Imports.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"documentation-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Documentation","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Update overview.Rmd. Update operations vignette.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9012","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9012 (2023-12-08)","text":"densify necessary. != 0, +/-. toDbDense() previously updated table value. change update reference via VIEW creation table named ‘dense’.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9012","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9012 (2023-12-08)","text":"Add dbListTables().","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9012","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9012 (2023-12-08)","text":"Update docs. Update gitignore.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9011","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9011 (2023-12-08)","text":"Fix incorrect aggregate operations. Fixes con slot removal.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9011","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9011 (2023-12-08)","text":"Add get_con(). Add dbDisconnect() generic. Update accessors.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9011","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9011 (2023-12-08)","text":"Update vignettes. Update README. Update gitignore. Update docs. 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