ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [cbind, rbind]
HenrikBengtsson opened this issue · comments
$ for pkg in $pkgs; do echo "$pkg:"; (cd "$pkg"; grep -E "^[ \t]*[^#].*[cr]bind" -- */*.R | grep -vF stringsAsFactors;); echo; read -r -p "Press ENTER to continue ..."; done
aroma.affymetrix:
R/AffymetrixCdfFile.computeAffinities.R: A <- cbind(charMtrx[1,,drop=TRUE] %*% affinity.basis.matrix,
R/AffymetrixCdfFile.computeAffinities.R: A <- cbind(charMtrx[1,,drop=TRUE] %*% affinity.basis.matrix,
R/AffymetrixCdfFile.getAlleleProbePairs3.R: data <- cbind(unitsChunk[uu], group, values)
R/AffymetrixCdfFile.getCellQuartets.R: cellsUUMerged <- cbind(cellsUUMerged, cellsGG)
R/AffymetrixCdfFile.getProbeSequenceData.R: data <- cbind(cell=cells, data)
R/AffymetrixCdfFile.getUnitGroupCellMap.R: map <- cbind(ugcMap, cpMap)
R/AffymetrixCdfFile.MONOCELL.R: mergedMap <- cbind(ugcMap[[1]], cellM=ugcMap[[2]][rr,"cell"])
R/AffymetrixCdfFile.UNIQUE.R: mergedMap <- cbind(ugcMap[[1]], cellM=ugcMap[[2]][rr,"cell"])
R/AffymetrixCelFile.PLOT.R: ma <- cbind(x=x, ma)
R/AffymetrixCelSet.writeSgr.R: data <- cbind(ch, pos, data)
R/AffymetrixNetAffxCsvFile.XTRS.R: dataKK <- Reduce(rbind, dataList[idxs])
R/AffymetrixNetAffxCsvFile.XTRS.R: data <- cbind(unitName=unitNames, index=idxs, data)
R/AlleleSummation.R: data <- cbind(cell=cells, data)
R/AlleleSummation.R: data <- cbind(cell=cells, intensities=y, stdvs=sd)
R/AllelicCrosstalkCalibration.getSetsOfProbes.R: snpsT$all <- cbind(snpsT$all, snps[[kk]])
R/ChipEffectFile.R: map <- cbind(ugcMap, cpMap)
R/ChipEffectFile.R: data <- cbind(map, data)
R/ChipEffectFile.xam.R: xam <- cbind(x=x, am)
R/ChipEffectNnn.extractChromosomalDataFrame.R: data <- cbind(dataHead, gp, dataTail)
R/ChipEffectSet.calculateBaseline.R: ds <- cbind(intensities=ds, cell=cells)
R/ChipEffectSet.calculateBaseline.R: ds <- cbind(intensities=ds, cell=cells)
R/ChipEffectSet.xam.R: xam <- cbind(x=x, am)
R/ExonRmaPlm.calculateWeights.R: y <- do.call(rbind, lapply(unit, FUN=.subset2, "eps"))
R/FirmaFile.R: data <- cbind(map, data)
R/fitPlasqUnit.R: paramIndMat <- cbind(
R/MatNormalization.R: designMatrix <- cbind(nT, A, C, G, rowSums(A)^2, rowSums(C)^2, rowSums(G)^2, nT^2, log(as.integer(ms[,1])))
R/MatSmoothing.R: nullX <- cbind(neg=matScoreNeg, pos=matScorePos)
R/ParameterCelFile.extractNnn.R: data <- cbind(ugcMap, data)
R/ParameterCelFile.extractNnn.R: data <- cbind(ugNames, data)
R/ParameterCelSet.R: data <- cbind(ugcMap, data)
R/ParameterCelSet.R: data <- cbind(ugNames, data)
R/ResidualFile.R: data <- cbind(map, data)
R/SnpChipEffectNnn.extractCNT.R: dataHead <- cbind(ProbeSet=unitNames, dataHead)
R/SnpChipEffectNnn.extractCNT.R: data <- cbind(dataHead, data)
R/SnpInformation.R: data <- cbind(data[,-cc,drop=FALSE], lss)
R/UnitTypeScaleNormalization.R: data <- rbind(data, dataKK)
R/WeightsFile.R: data <- cbind(map, data)
$ pkg=aroma.affymetrix; echo "$pkg:"; (cd "$pkg"; grep -E "^[ \t]*[^#].*rbind" -- */*.R | grep -vF stringsAsFactors;)
aroma.affymetrix:
R/AffymetrixNetAffxCsvFile.XTRS.R: dataKK <- Reduce(rbind, dataList[idxs])
R/ExonRmaPlm.calculateWeights.R: y <- do.call(rbind, lapply(unit, FUN=.subset2, "eps"))
R/UnitTypeScaleNormalization.R: data <- rbind(data, dataKK)