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I am running SCEVAN like so:
library(SCEVAN) dat <- readRDS("TN-B1-4031.rds") SCEVAN::pipelineCNA(dat, sample = "TN-B1-4031", par_cores = 20, SUBCLONES = TRUE, plotTree = TRUE)
and it crashes with the following error:
Error in iteration 2: arguments imply differing number of rows: 0, 48
It only happens with some of my samples.
The data looks like this:
> dat[1:5,1:5] pal_2021_GSM4909285_1-0 pal_2021_GSM4909285_2-0 UQCR10 8 4 SPP1 0 0 HLA-DPB1 0 0 B2M 14 12 RAB14 2 1 pal_2021_GSM4909285_3-0 pal_2021_GSM4909285_4-0 UQCR10 0 10 SPP1 0 0 HLA-DPB1 0 0 B2M 1 10 RAB14 0 2 pal_2021_GSM4909285_5-0 UQCR10 2 SPP1 0 HLA-DPB1 0 B2M 2 RAB14 2
The data file can be downloaded here. Here is another smaller dataset that fails.
Here is the full log:
[1] " raw data - genes: 13253 cells: 1482" [1] "1) Filter: cells > 200 genes" [1] "low data quality" [1] "2) Filter: genes > 5% of cells" [1] "2451 genes past filtering" [1] "3) Annotations gene coordinates" The number of elements of the gene set is less than the minimum allowed. The number of elements of the gene set is less than the minimum allowed. The number of elements of the gene set is less than the minimum allowed. The number of elements of the gene set is less than the minimum allowed. ... <This line is repeated hundreds of times> ... The number of elements of the gene set is less than the minimum allowed. The number of elements of the gene set is less than the minimum allowed. The number of elements of the gene set is less than the minimum allowed. The number of elements of the gene set is less than the minimum allowed. [1] "found 30 confident non malignant cells" [1] "2378 genes annotated" [1] "4) Filter: genes involved in the cell cycle" [1] "2205 genes past filtering " [1] "5) Filter: cells > 5genes per chromosome " [1] "6) Log Freeman Turkey transformation" [1] "A total of 174 cells, 2205 genes after preprocessing" [1] "7) Measuring baselines (confident normal cells)" [1] "8) Smoothing data" [1] "9) Segmentation (VegaMC)" [1] "10) Adjust baseline" [1] "11) plot heatmap" [1] "found 48 tumor cells" [1] "time classify tumor cells: 23.0540297031403" [1] "found 2 subclones" percentage_cells_subsclone_1 percentage_cells_subsclone_2 0.4166667 0.5833333 [1] "Segmentation of subclone : 1" [1] "Segmentation of subclone : 2" $`wu-2021_4465_subclone1` Chr Start End Alteration segm.mean 2 1 16974502 31944856 -2 -0.215354 43 8 11795573 54147901 2 0.095991 46 8 97644179 144428563 2 0.122258 58 11 20363685 73761137 2 0.156543 63 12 752593 96269835 -2 -0.358043 68 12 112013316 123633766 2 0.159426 70 13 36998816 77019143 -2 -0.229887 71 13 95677139 114305817 -2 -0.238055 82 16 47154387 89968060 -2 -0.225194 85 17 7240014 57006768 -2 -0.301897 89 18 3247481 9285985 2 0.183345 91 18 56597208 80033949 2 0.137885 92 19 571277 4670370 2 0.048158 95 19 41956681 54194536 -2 -0.180862 98 20 44496221 63891545 -2 -0.201054 99 21 17593653 46665124 -2 -0.305551 13 2 177212563 197516737 -1 -0.064736 15 3 3148992 11771350 1 0.189506 16 3 13549131 48504826 -1 -0.062771 19 3 139517434 158829719 1 0.107402 47 9 121038 35732395 1 0.127720 80 16 4461680 24572863 1 0.186913 $`wu-2021_4465_subclone2` Chr Start End Alteration segm.mean 4 1 150265399 167937040 2 0.244055 53 12 752593 14803540 -2 -0.254675 55 12 46358189 107713167 -2 -0.116435 58 13 19633681 114305817 -2 -0.121179 68 16 3018445 30085377 2 0.244846 2 1 19640554 39487177 -1 -0.140271 13 3 33798352 52239260 -1 -0.105971 28 6 30345131 33711727 -1 -0.044950 50 11 62433542 65862026 1 0.188088 $`wu-2021_4465_clone` Chr Start End Alteration segm.mean 5 1 203795654 246768137 2 0.316165 10 2 264140 88750935 2 0.319686 14 2 201071433 241686991 2 0.236119 21 3 184174689 195584205 -2 -0.211273 22 4 1166932 155953917 -2 -0.238754 26 5 218241 55535050 2 0.193638 29 5 135570679 163519336 -2 -0.207735 34 6 42744481 169254044 2 0.213288 39 7 1152071 66958551 2 0.423589 49 9 99222064 137615360 -2 -0.269008 54 10 80131682 133373689 -2 -0.161538 56 11 307631 6619461 -2 -0.448406 61 11 102520508 134253370 -2 -0.088353 72 14 34981957 105480170 -2 -0.192639 75 15 24823637 58933653 -2 -0.194629 87 17 68035519 82730328 2 0.054674 93 19 5891276 17323301 -2 -0.202012 101 22 28794555 50628173 -2 -0.263656 Error in iteration 2: arguments imply differing number of rows: 0, 48
I have also tried reinstalling SCEVAN to the current version as of 8-Aug-2024.
R version 4.3.2 (2023-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) SCEVAN_1.0.1
The text was updated successfully, but these errors were encountered:
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I am running SCEVAN like so:
and it crashes with the following error:
Error in iteration 2: arguments imply differing number of rows: 0, 48
It only happens with some of my samples.
The data looks like this:
The data file can be downloaded here. Here is another smaller dataset that fails.
Here is the full log:
Full log
I have also tried reinstalling SCEVAN to the current version as of 8-Aug-2024.
The text was updated successfully, but these errors were encountered: