R/demo.R

In CharlesJB/rnaseq: Wrapper Functions for RNA-Seq Post-Processing

#' Get demo kallisto abundance files
#'
#' @param large If \code{TRUE}, returns 8 filenames. Otherwise returns 4.
#'
#' @return A vector of kallisto abundance filenames
#'
#' @examples
#' abundances <- get_demo_abundance_files()
#'
#' @export
get_demo_abundance_files <- function(large = FALSE) {
    stopifnot(is(large, "logical"))
    path <- system.file("extdata/quant/", package = "rnaseq")
    if (!large) {
        dir_names <- letters[1:4]
    } else {
        dir_names <- letters[1:8]
    }
    filenames <- paste0(path, "/", dir_names, "/abundance.tsv")
    names(filenames) <- dir_names
    filenames
}

#' Get demo txi file
#'
#' @param large If \code{TRUE}, txi matrices will contain 8 samples, otherwise
#' they will contain 4. Default: \code{FALSE}
#' @param txOut Return counts and abundance at the transcript level. Default:
#' \code{FALSE}
#' @param ercc Add ERCC counts to the txi?
#'
#' @return A txi object
#'
#' @examples
#' txi <- get_demo_txi()
#'
#' @export
get_demo_txi <- function(large = FALSE, txOut = FALSE, ercc = FALSE) {
    stopifnot(is(large, "logical"))
    stopifnot(is(txOut, "logical"))
    abundances <- get_demo_abundance_files(large)
    names(abundances) <- basename(dirname(abundances))
    demo_anno <- system.file("extdata/demo_anno.csv", package = "rnaseq")
    txi <- import_kallisto(abundances, anno = demo_anno, txOut = txOut)
    if (ercc) {
        m_ercc <- txi$counts[1:10,]
        rownames(m_ercc) <- ERCC92$id[1:10]
        txi$counts <- rbind(txi$counts, m_ercc)
        txi$abundance <- rbind(txi$abundance, m_ercc)
        txi$length <- rbind(txi$length, m_ercc)
        txi$anno <- rbind(txi$anno, ERCC92[1:10,])
    }
    txi
}

#' Get demo design
#'
#' @return A data.frame corresponding to the demo txi object. See
#'         ?get_demo_txi.
#'
#' @examples
#' design <- get_demo_design()
#'
#' @export
get_demo_design <- function() {
    data.frame(sample = letters[1:4], group = c("A", "A", "B", "B"))
}

#' Get demo kallisto quant dir
#'
#' @return The path to kallisto results
#'
#' @examples
#' dir_quant <- get_demo_kallisto_dir()
#'
#' @export
get_demo_kallisto_dir <- function() {
    system.file("extdata/quant", package = "rnaseq")
}

#' Get demo annotation file
#'
#' @return The path to the annotation file
#'
#' @examples
#' file_anno <- get_demo_anno_file()
#'
#' @export
get_demo_anno_file <- function() {
    system.file("extdata/demo_anno.csv", package = "rnaseq")
}

#' Get demo pca infos file
#'
#' @return The path to the pca infos file
#'
#' @examples
#' pca_infos <- get_demo_pca_infos_file()
#'
#' @export
get_demo_pca_infos_file <- function() {
    system.file("extdata/pca_infos.csv", package = "rnaseq")
}

#' Get demo metadata file
#'
#' @return The path to the metadata file
#'
#' @examples
#' metadata <- get_demo_metadata_file()
#'
#' @export
get_demo_metadata_file <- function() {
    system.file("extdata/metadata.csv", package = "rnaseq")
}

#' Get demo de_infos file
#'
#' @return The path to the DE infos file
#'
#' @examples
#' de_infos <- get_demo_de_infos_file()
#'
#' @export
get_demo_de_infos_file <- function() {
    system.file("extdata/de_infos.csv", package = "rnaseq")
}

#' Get demo volcano_infos file
#'
#' @return The path to the DE infos file
#'
#' @examples
#' volcano_infos <- get_demo_volcano_infos_file()
#'
#' @export
get_demo_volcano_infos_file <- function() {
    system.file("extdata/volcano_infos.csv", package = "rnaseq")
}