R/bgScores.R

In dvera/travis: R Utilities for Bed and BEdgRaphs

#' Retreive scores in bedGraph files
#'
#' \code{bgScores} returns a list of vectors containing the scores for intervals in a set of bedGraph files.
#'
#' @param bgFiles A character vector of paths to bedgraph files.
#' @param threads A positive integer specifying how many bams to process simultaneously.

bgScores <- function( bgFiles , threads=getOption("threads", 1L), sample=NULL, chrom=NULL, first=NULL ){

  options(scipen=9999)
  
  numbeds <- length(bgFiles)

  if( !is.null(sample) & !is.null(chrom) ){stop("must set sample or chrom or neither, but not both")}

  if(!is.null(sample)){
    stopifnot(is.numeric(sample), length(sample)==1,sample>0)
    cmdString <- paste("shuf -n",sample,bgFiles,"| cut -f 4")
  } else if( !is.null(chrom)){
    stopifnot(length(chrom)==1)
    cmdString <- paste0("grep -P '^",chrom,"\\t' ",bgFiles," | cut -f 4")
  } else if(!is.null(first) & is.numeric(first)){
    cmdString <- paste("head -n",first,bgFiles," | cut -f 4")
  } else{
    cmdString <- paste("cut -f 4",bgFiles)
  }

  res <- cmdRun( cmdString, threads, lines=TRUE)
  res <- lapply( res, as.numeric )
  names(res) <- basename(bgFiles)

  return(res)

}