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HenrikBengtsson / PSCBS

🔬 R package: Analysis of Parent-Specific DNA Copy Numbers
https://cran.r-project.org/package=PSCBS
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ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [data.frame] #56

Closed HenrikBengtsson closed 3 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

PSCBS:
R/AbstractCBS.PRUNE.R:    knownSegments <- data.frame(chromosome=chromosome, start=-Inf, end=+Inf)
R/AbstractCBS.PRUNE.R:    segsKK <- data.frame(chromosome=chrsKK, start=startsKK, end=endsKK)
R/AbstractCBS.PRUNE.R:    knownSegments <- data.frame(chromosome=chromosome, start=-Inf, end=+Inf)
R/AbstractCBS.R:  loci <- Arguments$getInstanceOf(loci, "data.frame")
R/AbstractCBS.R:  segments <- Arguments$getInstanceOf(segments, "data.frame")
R/AbstractCBS.R:setMethodS3("as.data.frame", "AbstractCBS", function(x, ...) {
R/callSegmentationOutliers.R:setMethodS3("callSegmentationOutliers", "data.frame", function(y, ...) {
R/callSegmentationOutliers.R:setMethodS3("dropSegmentationOutliers", "data.frame", function(y, ...) {
R/CBS.CALL.R:  callsL <- as.data.frame(callsL)
R/CBS.CALL.R:  regions <- as.data.frame(regions)
R/CBS.CALL.R:  res1 <- as.data.frame(res)
R/CBS.CALL.R:  genomeData <- as.data.frame(genomeData)
R/CBS.CALL.R:setMethodS3("encodeCalls", "data.frame", function(calls, flavor="UCSF", ...) {
R/CBS.EXTS.R:  data <- data.frame(
R/CBS.EXTS.R:  output <- data.frame(
R/CBS.EXTS.R:  class(data) <- "data.frame"
R/CBS.EXTS.R:  res <- as.data.frame(res)
R/CBS.PLOT.R:  segs <- as.data.frame(fitT)
R/CBS.PLOT.R:  .stop_if_not(inherits(genomeData, "data.frame"))
R/CBS.PRUNE.R:    segRowsP <- data.frame(startRow=c(1L, endRow[-n]+1L), endRow=endRow)
R/CBS.R:setMethodS3("as.data.frame", "CBS", function(x, ...) {
R/CBS.R:  cps <- data.frame(
R/CBS.R:  class(data) <- "data.frame"
R/CBS.SMOOTH.R:    dataTS <- data.frame(chromosome=chr, x=xS, count=count, y=yS)
R/DNAcopy.EXTS.R:  class(data) <- c("CNA", "data.frame")
R/DNAcopy.EXTS.R:  output <- data.frame(
R/findLargeGaps.R:    gaps <- data.frame(chromosome=integer(0L), start=xEmpty, end=xEmpty)
R/findLargeGaps.R:    gaps <- data.frame(start=xL+resolution, end=xR-resolution)
R/findLargeGaps.R:  .stop_if_not(is.data.frame(gaps))
R/findLargeGaps.R:setMethodS3("findLargeGaps", "data.frame", function(chromosome, ...) {
R/findNeutralCopyNumberState.R:    df <- data.frame(C=y, weights=weights)
R/gapsToSegments.R:setMethodS3("gapsToSegments", "data.frame", function(gaps, resolution=1L, minLength=0L, dropGaps=FALSE, ...) {
R/gapsToSegments.R:    knownSegments <- data.frame(chromosome=integer(1L), start=-Inf, end=+Inf)
R/gapsToSegments.R:    knownSegmentsCC <- data.frame(chromosome=chr, start=bps[1L,], end=bps[2L,])
R/gapsToSegments.R:  .stop_if_not(is.data.frame(knownSegments))
R/NonPairedPSCBS.R:  class(data) <- "data.frame"
R/PairedPSCBS.applyByRegion.R:    .stop_if_not(is.data.frame(dataRRN))
R/PairedPSCBS.applyByRegion.R:    .stop_if_not(is.data.frame(segRRN))
R/PairedPSCBS.applyByRegion.R:      dataRowsN <- as.data.frame(dataRowsN)
R/PairedPSCBS.applyByRegion.R:  CC <- data.frame(C1=C1, C2=C2)
R/PairedPSCBS.applyByRegion.R:  outputT <- as.data.frame(outputT)
R/PairedPSCBS.applyByRegion.R:  CC <- data.frame(CA=CA, CB=CB)
R/PairedPSCBS.applyByRegion.R:  outputT <- as.data.frame(outputT)
R/PairedPSCBS.BOOT.R:      .stop_if_not(is.data.frame(stats))
R/PairedPSCBS.callAB.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.callAB.R:    segs <- as.data.frame(fit)
R/PairedPSCBS.callAB.R:    segs <- as.data.frame(fit)
R/PairedPSCBS.callAB.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.callCopyNeutral.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.callCopyNeutral.R:    segs <- as.data.frame(fit)
R/PairedPSCBS.callCopyNeutral.R:    stats <- data.frame(tolerance=tols, delta=NA_real_, count=NA_integer_)
R/PairedPSCBS.callGNL.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.callGNL.R:    segs <- as.data.frame(fit)
R/PairedPSCBS.callGNL.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.callGNL.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.callLOH.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.callLOH.R:    segs <- as.data.frame(fit)
R/PairedPSCBS.callLOH.R:    segs <- as.data.frame(fit)
R/PairedPSCBS.callLOH.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.callLOH.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.CALL.R:  callsL <- as.data.frame(callsL)
R/PairedPSCBS.estimateDeltaAB.R:  segs <- as.data.frame(this)
R/PairedPSCBS.estimateDeltaAB.R:  segs <- as.data.frame(this)
R/PairedPSCBS.estimateDeltaAB.R:  segs <- as.data.frame(this)
R/PairedPSCBS.extractSegmentDataByLocus.R:  dataL <- as.data.frame(dataL)
R/PairedPSCBS.EXTS3.R:  data.frame(C1=C1, C2=C2)
R/PairedPSCBS.PLOT2.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.PLOT2.R:      segs <- as.data.frame(fit)
R/PairedPSCBS.PLOT,many.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.PLOT.R:  segs <- as.data.frame(fit)
R/PairedPSCBS.PLOT.R:  segs <- as.data.frame(fitT)
R/PairedPSCBS.PLOT.R:  segs <- as.data.frame(fitT)
R/PairedPSCBS.PLOT.R:  res <- as.data.frame(res)
R/PairedPSCBS.R:  class(data) <- "data.frame"
R/PSCBS.R:setMethodS3("as.data.frame", "PSCBS", function(x, ...) {
R/PSCBS.R:  cps <- data.frame(
R/segmentByCBS.R:    knownSegments <- data.frame(chromosome=integer(0), start=integer(0), end=integer(0))
R/segmentByCBS.R:  if (!is.data.frame(knownSegments)) {
R/segmentByCBS.R:    throw("Argument 'knownSegments' is not a data.frame: ", class(knownSegments)[1])
R/segmentByCBS.R:  data <- data.frame(chrom=chrom, x=x, y=y, index=index)
R/segmentByCBS.R:          knownSegmentsKK <- data.frame(chromosome=chromosomeKK, start=-Inf, end=+Inf)
R/segmentByCBS.R:        verbose && print(verbose, head(as.data.frame(fit)), level=-10)
R/segmentByCBS.R:        verbose && print(verbose, tail(as.data.frame(fit)), level=-10)
R/segmentByCBS.R:    segs <- as.data.frame(fit)
R/segmentByCBS.R:    knownSegments <- data.frame(chromosome=currChromosome, start=-Inf, end=+Inf)
R/segmentByCBS.R:    dataS <- data.frame(y=c(0,0), chromosome=c(1,2), x=c(0,0))
R/segmentByCBS.R:        segs <- as.data.frame(fit)
R/segmentByCBS.R:  class(data) <- c("data.frame")
R/segmentByCBS.R:setMethodS3("segmentByCBS", "data.frame", function(y, ...) {
R/segmentByNonPairedPSCBS.R:  verbose && print(verbose, head(as.data.frame(fit)))
R/segmentByNonPairedPSCBS.R:  verbose && print(verbose, tail(as.data.frame(fit)))
R/segmentByNonPairedPSCBS.R:setMethodS3("segmentByNonPairedPSCBS", "data.frame", function(CT, ...) {
R/segmentByPairedPSCBS.R:    knownSegments <- data.frame(chromosome=integer(0), start=integer(0), end=integer(0))
R/segmentByPairedPSCBS.R:  if (!is.data.frame(knownSegments)) {
R/segmentByPairedPSCBS.R:    throw("Argument 'knownSegments' is not a data.frame: ", class(knownSegments)[1])
R/segmentByPairedPSCBS.R:  data <- data.frame(chromosome=chromosome, x=x, CT=CT)
R/segmentByPairedPSCBS.R:        verbose && print(verbose, head(as.data.frame(fit)))
R/segmentByPairedPSCBS.R:        verbose && print(verbose, tail(as.data.frame(fit)))
R/segmentByPairedPSCBS.R:    segs <- as.data.frame(fit)
R/segmentByPairedPSCBS.R:      knownSegmentsT <- data.frame(chromosome=currChromosome, start=xStart, end=xEnd)
R/segmentByPairedPSCBS.R:  verbose && print(verbose, head(as.data.frame(fit)))
R/segmentByPairedPSCBS.R:  verbose && print(verbose, tail(as.data.frame(fit)))
R/segmentByPairedPSCBS.R:setMethodS3("segmentByPairedPSCBS", "data.frame", function(CT, ...) {
tests/findLargeGaps.R:data <- data.frame(chromosome=0L, x=x)
tests/findLargeGaps.R:stopifnot(is.data.frame(gaps))
tests/findLargeGaps.R:stopifnot(is.data.frame(segs))
tests/findLargeGaps.R:stopifnot(is.data.frame(gaps))
tests/findLargeGaps.R:stopifnot(is.data.frame(segs))
tests/findLargeGaps.R:stopifnot(is.data.frame(gaps))
tests/findLargeGaps.R:stopifnot(is.data.frame(segs))
tests/findLargeGaps.R:stopifnot(is.data.frame(gaps))
tests/findLargeGaps.R:stopifnot(is.data.frame(segs))
tests/PairedPSCBS,boot.R:knownSegments <- data.frame(
tests/segmentByCBS,calls.R:data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT)
tests/segmentByCBS,futures.R:  data[[cc]] <- data.frame(chromosome=cc, y=y, x=x)
tests/segmentByCBS,futures.R:  knownSegments[[cc]] <- data.frame(
tests/segmentByCBS,median.R:data <- data.frame(chromosome=1L, x=x, y=y)
tests/segmentByCBS,prune.R:  data[[chr]] <- data.frame(chromosome=chr, x=x, y=y)
tests/segmentByCBS.R:knownSegments <- data.frame(
tests/segmentByCBS.R:knownSegments <- data.frame(
tests/segmentByCBS.R:knownSegments <- data.frame(
tests/segmentByCBS.R:knownSegments <- data.frame(
tests/segmentByCBS.R:knownSegments <- data.frame(
tests/segmentByCBS,report.R:data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT)
tests/segmentByCBS,shiftTCN.R:  data[[chr]] <- data.frame(chromosome=chr, y=y, x=x)
tests/segmentByCBS,weights.R:data <- data.frame(chromosome=1L, x=x, y=y)
tests/segmentByCBS,weights.R:knownSegments <- data.frame(
tests/segmentByCBS,weights.R:knownSegments <- data.frame(
tests/segmentByCBS,weights.R:knownSegments <- data.frame(
tests/segmentByCBS,weights.R:knownSegments <- data.frame(
tests/segmentByCBS,weights.R:knownSegments <- data.frame(
tests/segmentByPairedPSCBS.R:knownSegments <- data.frame(
tests/segmentByPairedPSCBS.R:knownSegments <- data.frame(
tests/segmentByPairedPSCBS.R:knownSegments <- data.frame(
tests/segmentByPairedPSCBS.R:knownSegments <- data.frame(
HenrikBengtsson commented 3 years ago

Seems to work as-is. wont-fix