CLEANUP: Partial argument names

[HenrikBengtsson]

seq() -> seq_along() and seq_len()

• We use seq(length=n) but should be seq(length.out=n) or these days seq_len(n).
• We use seq(along=x) but should be seq(along.with=x) or these days seq_along(x).

seq() calls to be updated (manually filtered):

$ grep -F "seq(" R/*.R
R/applyCdfBlocks.R:  for (uu in seq(along=cdf)) {
R/applyCdfGroups.R:  for (uu in seq(along=cdf)) {
R/arrangeCelFilesByChipType.R:  for (ii in seq(along=pathnames)) {
R/cdfAddBaseMmCounts.R:  for (gg in seq(along=groups)) {
R/cdfAddPlasqTypes.R:  for (gg in seq(along=groups)) {
R/cdfMergeAlleles.R:    for (ff in seq(length=nbrOfFields)) {
R/cdfMergeToQuartets.R:    for (ff in seq(length=nbrOfFields)) {
R/compareCdfs.R:  units <- seq(length=h1$nqcunits);
R/compareCdfs.R:  units <- seq(length=h1$nunits);
R/findFiles.R:  for (kk in seq(along=paths)) {
R/readCcgHeader.R:  for (kk in seq(length=nbrOfParams)) {
R/readCcgHeader.R:  for (kk in seq(length=nbrOfParents)) {
R/readCcg.R:  for (gg in seq(length=.fileHeader$nbrOfDataGroups)) {
R/readCcg.R:    for (kk in seq(along=dss)) {
R/readCcg.R:  for (kk in seq(length=nbrOfParams)) {
R/readCcg.R:  for (cc in seq(length=nbrOfColumns)) {
R/readCcg.R:  for (cc in seq(length=nbrOfColumns)) {
R/readCcg.R:      for (pp in seq(length=nrow(value))) {
R/readCdfCellIndices.R:    for (uu in seq(along=cdf)) {
R/readCdfCellIndices.R:    for (uu in seq(along=cdf)) {
R/readCdfCellIndices.R:    for (uu in seq(along=cdf)) {
R/readCdfDataFrame.R:    units <- seq(along=cdf);  ## FIX ME
R/readCdfDataFrame.R:  for (uu in seq(along=cdf)) {
R/readCdfDataFrame.R:      ggs <- seq(along=groups);
R/readCdfDataFrame.R:      keep <- which(seq(along=groups) %in% groupIdxs);
R/readCdfDataFrame.R:    for (gg in seq(along=ggs)) {
R/readCdfDataFrame.R:        keep <- (seq(length=nrow(cellData)) %in% cells);
R/readCdfDataFrame.R:    for (gg in seq(along=groups)) {
R/readCdfDataFrame.R:  for (uu in seq(along=cdf)) {
R/readCdf.R:        for (uu in seq(along=cdf)) {
R/readCdf.R:        for (uu in seq(along=cdf)) {
R/readCdf.R:        for (uu in seq(along=cdf)) {
R/readCdfUnits.R:    for (uu in seq(along=cdf)) {
R/readCdfUnits.R:    for (uu in seq(along=cdf)) {
R/readCdfUnits.R:    for (uu in seq(along=cdf)) {
R/readCelUnits.R:  for (kk in seq(length=nbrOfArrays)) {
R/readCelUnits.R:          dimnames <- list(seq(length=dim));
R/writeCdfQcUnits.R:  for(kk in seq(length=nbrOfQCUnits)) {
R/writeCdfUnits.R:  for(kk in seq(length=nbrOfUnits)) {

[HenrikBengtsson]

Fixed. Most could be fixed using:

for ff in $(grep -l -F "seq(along=" R/*.R); do echo $ff; sed -i.bak s/seq\(along=/seq_along\(/g $ff; done
for ff in $(grep -l -F "seq(length=" R/*.R); do echo $ff; sed -i.bak s/seq\(length=/seq_len\(/g $ff; done