R/getTotalMapped.R

In derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

#' Calculate the total number of mapped reads
#'
#' For a given BAM calculate the total number of mapped reads and for a BigWig
#' file calculate the area under the curve (AUC), which is related to the
#' number of mapped reads: the exact relationship depends on whether the
#' aligner soft clips reads and/or if the length of the reads is the same.
#' If you use the 'chrs' argument you can choose to only consider the
#' information for your chromosomes of interest. For example, you can exclude
#' the mitocondrial chromosome.
#'
#' @param rawFile Either a BAM file or a BigWig file.
#' @param chrs If `NULL`, all the chromosomes will be used. Otherwise,
#' only those in `chrs` will be used.
#'
#' @return The total number of mapped reads for a BAM file or the AUC for a
#' BigWig file in a single element vector.
#'
#' @author Leonardo Collado-Torres
#'
#' @export
#' @importFrom rtracklayer BigWigFileList BigWigFile
#' @importMethodsFrom rtracklayer import import.bw
#' @importFrom Rsamtools idxstatsBam BamFileList
#'
#' @examples
#'
#' ## Get the total number of mapped reads for an example BAM file:
#' bam <- system.file("extdata", "genomeData", "ERR009102_accepted_hits.bam",
#'     package = "derfinder", mustWork = TRUE
#' )
#' getTotalMapped(bam)
getTotalMapped <- function(rawFile, chrs = NULL) {
    stopifnot(length(rawFile) == 1)

    ## Guess the input type
    if (is(rawFile, "BigWigFileList") | is(rawFile, "BigWigFile") | grepl("bw$|bigwig$", tolower(rawFile))) {
        inputType <- "BigWig"
    } else if (is(rawFile, "BamFileList") | is(rawFile, "BamFile") | grepl("bam$", tolower(rawFile))) {
        inputType <- "bam"
    }
    stopifnot(inputType %in% c("bam", "BigWig"))

    if (inputType == "bam") {
        info <- idxstatsBam(rawFile)
        if (!is.null(chrs)) {
            info <- subset(info, seqnames %in% chrs)
        }
        res <- sum(info$mapped)
    } else if (inputType == "BigWig") {
        if (.Platform$OS.type == "windows") {
            warning("As of rtracklayer 1.25.16, BigWig is not supported on Windows. Thus loading data from BigWig files will most likely fail!")
        }
        gr <- import.bw(rawFile)

        if (!is.null(chrs)) {
            gr <- gr[seqnames(gr) %in% chrs]
        }

        res <- sum(width(gr) * gr$score)
    }
    return(res)
}