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HenrikBengtsson / aroma.affymetrix

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets
https://cran.r-project.org/package=aroma.affymetrix
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ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [cbind, rbind] #39

Open HenrikBengtsson opened 4 years ago

HenrikBengtsson commented 4 years ago 
$ 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)
HenrikBengtsson commented 4 years ago 
$ 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)