# 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
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.