R/matrix.R

In pachterlab/sleuth: Tools for investigating RNA-Seq

#
#    sleuth: inspect your RNA-Seq with a pack of kallistos
#
#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
#
#    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 3 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, see <http://www.gnu.org/licenses/>.

#' Convert a sleuth object to matrix
#'
#' Convert a sleuth object to a matrix with the condition names.
#'
#' @param obj a \code{sleuth} object
#' @param which_df character vector of length one. Which type of data to use
#' ("obs_norm" or "obs_raw")
#' @param which_units character vector of length one. Which units to use ("tpm"
#' or "est_counts" (for transcript-level analyses) or "scaled_reads_per_base" (for gene-level analyses))
#' @return a matrix which contains a matrix of target_ids and transcript (or gene) expression in \code{which_units}.
#'   Note this currently does not support returning raw values for gene-level counts or TPMs.
#' @examples
#' sleuth_matrix <- sleuth_to_matrix(sleuth_obj, 'obs_norm', 'tpm')
#' head(sleuth_matrix) # look at first 5 transcripts, sorted by name
#' @export
sleuth_to_matrix <- function(obj, which_df, which_units) {
  if ( !(which_df %in% c("obs_norm", "obs_raw")) ) {
    stop("Invalid object")
  }
  if ( !(which_units %in% c("tpm", "est_counts", "scaled_reads_per_base")) ) {
    stop("Invalid units")
  }

  which_units <- check_quant_mode(obj, which_units)

  if (obj$gene_mode && which_df == "obs_raw") {
    warning("This object is in gene mode, and the raw values are ",
            "transcripts. Using 'obs_norm' instead.")
    which_df <- "obs_norm"
  }

  data <- as.data.frame(obj[[which_df]])

  res <- list()

  s_data <- dplyr::select_(data, "target_id", "sample", which_units)
  s_data <- tidyr::spread_(s_data, "sample", which_units)
  rownames(s_data) <- s_data$target_id
  s_data$target_id <- NULL
  s_data <- as.matrix(s_data)

  s_data
}