R/getWinCounts.R

In ZhenxingGuo0015/TRESS: Toolbox for mRNA epigenetics sequencing analysis

## get read counts for given genomic windows
# getWinCounts <- function(files, wins,
#                          filetype = c("bed", "bam", "GRanges")
#                          ) {
#   if((!is.data.frame(wins)) & is(wins)[1]!="GRanges")
#     stop("Input genomic intervals must be a GRanges or data frame!")
#   if(is.data.frame(wins)) wins = import(wins)
#   counts = matrix(0, nrow = length(wins), ncol = length(files))
#   for(i in seq_len(length(files))) {
#     if(filetype!= "GRanges"){
#       if(filetype == "bam")
#         reads = read.BAM(files[i])
#       else if(filetype == "bed")
#         reads = import(files[i])
#       }else if(filetype == "GRanges"){
#         ### data in datasetTRES package
#         reads = get(files[i])
#         }
#     #### ended
#     counts[,i] = countOverlaps(wins,reads)
#     }
#   colnames(counts) = files
#   counts
#   }

getWinCounts <- function(files, wins,
                         filetype = c("bed", "bam", "GRanges")
                         ) {
  if((!is(wins, "data.frame")) & !is(wins[1], "GRanges"))
    stop("Input genomic intervals must be a GRanges or data frame!")
  if(is(wins, "data.frame")) wins = import(wins)
  counts = matrix(0, nrow = length(wins), ncol = length(files))
  for(i in seq_len(length(files))) {
    if(filetype!= "GRanges"){   
      if(filetype == "bam")
        reads = read.BAM(files[i])
      else if(filetype == "bed")
        reads = import(files[i])
    }else if(filetype == "GRanges"){
      ### data in datasetTRES package
      reads = get(files[i])
    }
    #### ended
    counts[,i] = countOverlaps(wins,reads)
  }
  colnames(counts) = files
  counts
}