Mismatch between rownames of tagMatrix and windows indexes

[lufce]

Dear Pr Guangchuang Yu,

Thank you for developing a useful library.
But, there seems to be a bug in getTagMatrix.internal function in tagMatrix.R.

# --- from Line 521
  windows <- subsetByOverlaps(windows, cov.width,
                              type="within", ignore.strand=FALSE)
  
  chr.idx <- intersect(names(peak.cov),
                       unique(as.character(seqnames(windows))))
  
  peakView <- Views(peak.cov[chr.idx], as(windows, "IntegerRangesList")[chr.idx])
  tagMatrixList <- lapply(peakView, function(x) t(viewApply(x, as.vector)))
  tagMatrix <- do.call("rbind", tagMatrixList)
  
  ## get the index of windows, that are reorganized by as(windows, "IntegerRangesList")
  idx.list <- split(1:length(windows),  as.factor(seqnames(windows)))
  idx <- do.call("c", idx.list)
  
  rownames(tagMatrix) <- idx
  tagMatrix <- tagMatrix[order(idx),]

I guess it tries to copy the indexes of windows to tagMatrix's rownames.
But, it won't work because peakView and idx.list do not have the same order of chromosome numbers.

• peakView: $chr1, $chr2, $chr3, ...
• idx.list: $chr1, $chr10, $chr11, ...

It'll cause to disconnect between tagMatrix index and window index.

I suggest the fixed code below, but I don't know it's the best way.

# --- from Line 521
  windows <- subsetByOverlaps(windows, cov.width,
                              type="within", ignore.strand=FALSE)
  
  chr.idx <- intersect(names(peak.cov),
                       unique(as.character(seqnames(windows))))
  
  peakView <- Views(peak.cov[chr.idx], as(windows, "IntegerRangesList")[chr.idx])
  tagMatrixList <- lapply(peakView, function(x) t(viewApply(x, as.vector)))
  tagMatrix <- do.call("rbind", tagMatrixList)
  
  ## get the index of windows, that are reorganized by as(windows, "IntegerRangesList")
  idx.list <- split(1:length(windows),  as.factor(seqnames(windows)))
  # ---modification
  # idx <- do.call("c", idx.list)
  idx = c()
  for(i in chr.idx){
    idx = c(idx, idx.list[[i]])
  }
  # --- end modification
  
  rownames(tagMatrix) <- idx
  tagMatrix <- tagMatrix[order(idx),]