remove data.table and R.utils

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: raer
 Type: Package
 Title: RNA editing tools in R
-Version: 1.1.3
+Version: 1.1.2
 Authors@R: c(
     person("Kent", "Riemondy", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0750-1273")),
@@ -22,7 +22,6 @@ License: MIT + file LICENSE
 Imports: 
     stats,
     methods,
-    data.table,
     GenomicRanges,
     IRanges,
     Rsamtools,
@@ -38,7 +37,6 @@ Imports:
     BiocParallel,
     rtracklayer,
     Matrix,
-    R.utils,
     cli
 Suggests:
     testthat (>= 3.0.0),
@@ -65,7 +63,7 @@ SystemRequirements:
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 URL: https://rnabioco.github.io/raer, https://github.com/rnabioco/raer
 BugReports: https://github.com/rnabioco/raer/issues
 biocViews:

NAMESPACE

@@ -57,7 +57,6 @@ importFrom(IRanges,extractList)
 importFrom(IRanges,subsetByOverlaps)
 importFrom(Matrix,colSums)
 importFrom(Matrix,sparseMatrix)
-importFrom(R.utils,gzip)
 importFrom(Rsamtools,BamFile)
 importFrom(Rsamtools,BamFileList)
 importFrom(Rsamtools,FaFile)
@@ -71,7 +70,6 @@ importFrom(Rsamtools,seqinfo)
 importFrom(S4Vectors,aggregate)
 importFrom(S4Vectors,unstrsplit)
 importFrom(SingleCellExperiment,SingleCellExperiment)
-importFrom(data.table,fread)
 importFrom(methods,"slot<-")
 importFrom(methods,as)
 importFrom(methods,is)

R/sc-pileup.R

@@ -336,7 +336,8 @@ get_sc_pileup <- function(bamfn, index, id, sites, barcodes,
 #' intervals, whereas `index`` will only add row indices to the rownames.
 #' @returns a `SingleCellExperiment` object populated with `nRef` and `nAlt`
 #' assays.
-#'
+#' 
+#' @importFrom utils read.table
 #' @examples
 #' library(Rsamtools)
 #' library(GenomicRanges)
@@ -359,18 +360,16 @@ get_sc_pileup <- function(bamfn, index, id, sites, barcodes,
 #'
 #' unlink(bai)
 #'
-#' @importFrom data.table fread
 #' @importFrom Matrix sparseMatrix
 #' @importFrom SingleCellExperiment SingleCellExperiment
-#' @importFrom R.utils gzip
 #' @export
 read_sparray <- function(mtx_fn, sites_fn, bc_fn,
     site_format = c("coordinate", "index")) {
     if (!file.size(sites_fn) > 0) {
         return(SingleCellExperiment::SingleCellExperiment())
     }
 
-    rnames <- data.table::fread(sites_fn,
+    rnames <- read.table(sites_fn,
         sep = "\t",
         col.names = c(
             "index", "seqnames", "start",
@@ -380,7 +379,7 @@ read_sparray <- function(mtx_fn, sites_fn, bc_fn,
             "integer", "character", "integer",
             "integer", "character", "character"
         ),
-        data.table = FALSE
+        row.names = NULL
     )
     site_format <- match.arg(site_format)
 
@@ -404,7 +403,7 @@ read_sparray <- function(mtx_fn, sites_fn, bc_fn,
     n_sp_cols <- 2 + length(sp_mtx_names)
 
     if (file.size(mtx_fn) > 0) {
-        dt <- data.table::fread(mtx_fn,
+        dt <- read.table(mtx_fn,
             sep = " ",
             colClasses = "integer",
             skip = n_skip,
@@ -443,6 +442,7 @@ read_sparray <- function(mtx_fn, sites_fn, bc_fn,
     res
 }
 
+#' @importFrom utils write.table
 write_sparray <- function(sce, mtx_fn, sites_fn, bc_fn) {
     if (!all(c("nRef", "nAlt") %in% assayNames(sce))) {
         cli::cli_abort("missing required asssays nRef or nAlt")
@@ -474,7 +474,6 @@ write_sparray <- function(sce, mtx_fn, sites_fn, bc_fn) {
         mtx_fn
     )
 
-    mtx <- matrix(0L, nrow = dim(nref_trpl)[1], ncol = 4L)
     mtx <- cbind(nref_trpl, nalt = nalt_trpl$x)
 
     write.table(mtx, 

tests/testthat/test_aei.R

@@ -1,4 +1,4 @@
-pkgs <- c("Rsamtools", "data.table", "Biostrings")
+pkgs <- c("Rsamtools", "Biostrings")
 msg <- lapply(pkgs, function(x) {
     suppressPackageStartupMessages(library(x, character.only = TRUE))
 })
@@ -29,13 +29,17 @@ test_that("calc_aei basic options work", {
     expect_true(ag_aei["wt"] > ag_aei["ko"])
 
     x <- aei$AEI_per_chrom
-    setDT(x)
-    pc_aei <- x[, 100 * (sum(alt) / sum(alt + ref)), by = .(allele, bam_file)]
-    pc_aei <- dcast(pc_aei, bam_file ~ allele, value.var = "V1")
-    pc_aei <- as.data.frame(pc_aei)
-    rownames(pc_aei) <- pc_aei$bam_file
-    pc_aei$bam_file <- NULL
-    expect_true(identical(pc_aei, as.data.frame(aei$AEI)))
+    xx <- lapply(split(x, ~ allele + bam_file), function(x) {
+        xx <- 100 * (sum(x$alt) / sum(x$alt + x$ref))
+        data.frame(allele = unique(x$allele),
+                   bam_file = unique(x$bam_file),
+                   total = xx)
+    }) |> do.call(rbind, args = _)
+    xx <- reshape(xx, idvar = c("bam_file"), v.names = "total", timevar = "allele", direction = "wide")
+    rownames(xx) <- xx$bam_file
+    xx$bam_file <- NULL
+    colnames(xx) <- sub("total.", "", colnames(xx))
+    expect_true(identical(data.frame(xx), as.data.frame(aei$AEI)))
 
     aei <- calc_AEI(unname(bams), fafn, mock_alu_ranges)
     expect_true(all(rownames(aei$AEI) == unname(bams)))