R/fullCoverage.R

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

#' Load the unfiltered coverage information from a group of BAM files and a
#' list of chromosomes
#'
#' For a group of samples this function reads the coverage information for
#' several chromosomes directly from the BAM files. Per chromosome, it merges
#' the unfiltered coverage by sample into a DataFrame. The end result is a list
#' with one such DataFrame objects per chromosome.
#'
#' @param files A character vector with the full path to the sample BAM files
#' (or BigWig files).
#' The names are used for the column names of the DataFrame. Check
#' [rawFiles] for constructing `files`. `files` can also be a
#' `BamFileList` object created with [BamFileList][Rsamtools::BamFile-class] or a
#' `BigWigFileList` object created with [BigWigFileList][rtracklayer::BigWigFile].
#' @param chrs The chromosome of the files to read. The format has to match the
#' one used in the input files.
#' @param bai The full path to the BAM index files. If `NULL` it is
#' assumed that the BAM index files are in the same location as the BAM files
#' and that they have the .bai extension. Ignored if `files` is a
#' `BamFileList` object.
#' @param chrlens The chromosome lengths in base pairs. If it's `NULL`,
#' the chromosome length is extracted from the BAM files. Otherwise, it should
#' have the same length as `chrs`.
#' @param outputs This argument is passed to the `output` argument of
#' [loadCoverage]. If `NULL` or `'auto'` it is then recycled.
#' @inheritParams loadCoverage
#' @param ... Arguments passed to other methods and/or advanced arguments.
#' Advanced arguments:
#' \describe{
#' \item{verbose }{ If `TRUE` basic status updates will be printed along
#' the way.}
#' \item{mc.cores }{ How many cores to use for reading the chromosome
#' information. There's no benefit of using a number greater than the number
#' of chromosomes. Also note that your harddisk speed will limit how much
#' you get from using a higher `mc.cores` value.}
#' \item{mc.cores.load }{ Controls the number of cores to be used per chr for
#' loading the data which is only useful in the scenario that you are loading
#' in genome tiles. If not supplied, it uses `mc.cores` for
#' [loadCoverage]. Default: 1. If you are using genome tiles, the total
#' number of cores you'll use will be `mc.cores` times
#' `mc.cores.load`.}
#' }
#' Passed to [loadCoverage], [define_cluster] and
#' [extendedMapSeqlevels].
#' Note that [filterData] is used internally
#' by [loadCoverage] (and hence [fullCoverage]) and has the important
#' arguments `totalMapped` and `targetSize` which can be used to
#' normalize the coverage by library size. See [getTotalMapped] for
#' calculating `totalMapped`.
#'
#' @return A list with one element per chromosome.
#' \describe{ Each element is a DataFrame with the coverage information
#' produced by [loadCoverage].
#' }
#'
#' @seealso [loadCoverage], [filterData], [getTotalMapped]
#'
#' @author Leonardo Collado-Torres
#' @export
#' @importFrom BiocParallel bplapply
#' @importFrom GenomeInfoDb mapSeqlevels
#'
#' @examples
#' datadir <- system.file("extdata", "genomeData", package = "derfinder")
#' files <- rawFiles(
#'     datadir = datadir, samplepatt = "*accepted_hits.bam$",
#'     fileterm = NULL
#' )
#' ## Shorten the column names
#' names(files) <- gsub("_accepted_hits.bam", "", names(files))
#'
#' ## Read and filter the data, only for 1 file
#' fullCov <- fullCoverage(files = files[1], chrs = c("21", "22"))
#' fullCov
#' \dontrun{
#' ## You can then use filterData() to filter the data if you want to.
#' ## Use bplapply() if you want to do so with multiple cores as shown below.
#' library("BiocParallel")
#' p <- SnowParam(2L)
#' bplapply(fullCov, function(x) {
#'     library("derfinder")
#'     filterData(x, cutoff = 0)
#' }, BPPARAM = p)
#' }
#'
fullCoverage <- function(files, chrs, bai = NULL, chrlens = NULL,
    outputs = NULL, cutoff = NULL, ...) {
    stopifnot(length(files) > 0)
    stopifnot(length(chrlens) == length(chrs) | is.null(chrlens))
    stopifnot(is.character(chrs))
    if (!is.null(outputs)) {
        stopifnot(length(outputs) == length(chrs) | outputs == "auto")
        if (outputs == "auto") {
            outputs <- rep("auto", length(chrs))
        }
    }

    ## Advanged argumentsa
    # @param verbose If \code{TRUE} basic status updates will be printed along the
    # way.
    verbose <- .advanced_argument("verbose", TRUE, ...)


    # @param mc.cores.load Controls the number of cores to be used per chr for
    # loading the data.
    mc.cores.load <- .advanced_argument(
        "mc.cores.load",
        .advanced_argument("mc.cores", getOption("mc.cores", 1L), ...), ...
    )


    ## Define cluster
    BPPARAM <- define_cluster(...)

    ## Subsetting function that runs loadCoverage
    loadChr <- function(idx, files, chrs, bai, chrlens, outputs, cutoff,
    mc.load, ...) {
        if (verbose) {
              message(paste(
                  Sys.time(), "fullCoverage: processing chromosome",
                  chrs[idx]
              ))
          }
        if (is.null(cutoff)) {
            res <- loadCoverage(
                files = files, chr = chrs[idx], cutoff = NULL,
                bai = bai, chrlen = chrlens[idx], output = outputs[idx],
                mc.cores = mc.load, ...
            )$coverage
        } else {
            res <- loadCoverage(
                files = files, chr = chrs[idx],
                cutoff = cutoff, bai = bai, chrlen = chrlens[idx],
                output = outputs[idx], mc.cores = mc.load, ...
            )
        }
        return(res)
    }
    result <- bplapply(seq_len(length(chrs)), loadChr,
        files = files,
        chrs = chrs, bai = bai, chrlens = chrlens, outputs = outputs,
        cutoff = cutoff, mc.load = mc.cores.load,
        ..., BPPARAM = BPPARAM
    )
    names(result) <- extendedMapSeqlevels(chrs, ...)

    ## Done
    return(result)
}