R/rawFiles.R

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

#' Construct full paths to a group of raw input files
#'
#' For a group of samples this function creates the list of paths to the raw
#' input files which can then be used in [loadCoverage]. The raw input
#' files are either BAM files or BigWig files.
#'
#' @param datadir The main directory where each of the `sampledirs` is a
#' sub-directory of `datadir`.
#' @param sampledirs A character vector with the names of the sample
#' directories. If `datadir` is `NULL` it is then assumed that
#' `sampledirs` specifies the full path to each sample.
#' @param samplepatt If specified and `sampledirs` is set to `NULL`,
#' then the directories matching this pattern in `datadir` (set to
#' `.` if it's set to `NULL`) are used as the sample directories.
#' @param fileterm Name of the BAM or BigWig file used in each sample. By
#' default it is set to `accepted_hits.bam` since that is the automatic
#' name generated when aligning with TopHat. If `NULL` it is then ignored
#' when reading the rawfiles. This can be useful if all the raw files are
#' stored in a single directory.
#'
#' @return A vector with the full paths to the raw files and sample names
#' stored as the vector names.
#'
#' @details This function can also be used to identify a set of BigWig files.
#'
#' @author Leonardo Collado-Torres
#' @export
#' @seealso [loadCoverage]
#' @examples
#' ## Get list of BAM files included in derfinder
#' datadir <- system.file("extdata", "genomeData", package = "derfinder")
#' files <- rawFiles(
#'     datadir = datadir, samplepatt = "*accepted_hits.bam$",
#'     fileterm = NULL
#' )
#' files
rawFiles <- function(datadir = NULL, sampledirs = NULL, samplepatt = NULL,
    fileterm = "accepted_hits.bam") {
    ## Determine the full paths to the sample directories
    if (!is.null(sampledirs)) {
        if (!is.null(datadir)) {
            ## Using sampledirs with datadir
            files <- sapply(sampledirs, function(x) {
                file.path(datadir, x)
            })
            names(files) <- sampledirs
        } else {
            ## Using only the sampledirs since datadir is NULL
            files <- sampledirs
            names(files) <- sampledirs
        }
    } else if (!is.null(samplepatt)) {
        if (is.null(datadir)) {
            ## This case assumes that the datadir is the current directory
            datadir <- "."
        }
        ## Identify the directories with this pattern
        files <- dir(path = datadir, pattern = samplepatt, full.names = TRUE)
        names(files) <- dir(
            path = datadir, pattern = samplepatt,
            full.names = FALSE
        )
    } else {
        stop("Either 'samplepatt' or 'sampledirs' must be non-NULL.")
    }

    ## Tell R which are the BAM files
    if (!is.null(fileterm)) {
        tmp <- file.path(files, fileterm)
        names(tmp) <- names(files)
        files <- tmp
    }

    ## Done
    return(files)
}