R/readWrite.R

In pachterlab/kma: KeepMeAround: Intron Retention Detection in RNA-Seq data

# Keep Me Around: Intron Retention Detection
# Copyright (C) 2015  Harold Pimentel <haroldpimentel@gmail.com>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

#' Get the columns from eXpress output
#'
#' Given a list of data.frames (all containing the same type of layout),
#'
#' @param aList a list of xprs data.frames
#' @param col the column you wish to extract
#' @param substring_replace replace this substring from the target_id
#' @return a data.frame with the particular column from express output
#' @export
getCol <- function(aList, col, column_ids, substring_replace = NULL)
{
    df <- data.frame(lapply(aList, function(x) x[col]))

    data.table::setnames(df, colnames(df), column_ids)

    df$target_id <- aList[[1]]$target_id

    if (!is.null(substring_replace))
        df$target_id <- sub(substring_replace, '', aList[[1]]$target_id)

    df
}

#' @export
read_express <- function(file_names, sample_names, condition_names,
    cols = c("tpm", "uniq_counts"), substring_replace = NULL)
{
    cat("Reading all eXpress data...\n")
    all_xprs <- lapply(file_names, fread, header = TRUE, stringsAsFactors = FALSE,
        data.table = FALSE)

    cat("Sorting...\n")
    all_xprs <- lapply(all_xprs, arrange, target_id)

    res <- lapply(cols, function(col){
        cat("Extracting column: ", col, "\n")
        getCol(all_xprs, col, sample_names, substring_replace)
        })

    names(res) <- cols
    res$all_data <- all_xprs
    res$condition <- condition_names
    res$sample <- sample_names

    res
}