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HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework
https://github.com/HenrikBengtsson/aroma.seq
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ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [data.frame] #52

Open HenrikBengtsson opened 4 years ago

HenrikBengtsson commented 4 years ago 
$ for pkg in $pkgs; do echo "$pkg:"; (cd "$pkg"; grep -E "^[ \t]*[^#].*data[.]frame" -- */*.R | grep -vF stringsAsFactors;); echo; read -r -p "Press ENTER to continue ..."; done

aroma.seq:
R/agsub.R:agsub <- function(pattern, replacement, x, ..., default=NA_character_, as=c("matrix", "list", "data.frame")) {
R/agsub.R:  } else if (as == "data.frame") {
R/BamDataFile.R:    stats <- data.frame(length=seqLength, mapped=countMapped, unmapped=countUnmapped)
R/BamDataFile.R:  data <- as.data.frame(data)
R/BwaIndexSet.R:  if (length(idx) == 0) return(data.frame())
R/CnvKitCopyNumberRatioFile.R:  data.frame(chromosome=chr, x=(data$start + data$end)/2, y=ploidy*2^data$log2, w=data$weight)
R/countNucleotides.R:  loci <- Arguments$getInstanceOf(loci, "data.frame")
R/countNucleotides.R:  loci <- Arguments$getInstanceOf(loci, "data.frame")
R/GatkAlleleCounting.R:      data <- data.frame(chromosome=chr, position=pos, counts)
R/segmentByPairedPSCBS.SeqzFileSet.R:  data <- data.frame(
R/segmentByPairedPSCBS.SeqzFileSet.R:setMethodS3("binForPSCBS", "data.frame", function(data, binSize, ..., verbose=FALSE) {
tests/agsub.R:for (as in c("list", "data.frame", "matrix")) {
tests/countNucleotides.R:loci <- data.frame(chromosome=chrs[1L], pos=1:100)
tests/countNucleotides.R:loci <- data.frame(chromosome=chrs, pos=1:100)
tests/countNucleotides.R:loci <- data.frame(chromosome=chrs[1L], pos=1:100)