data-raw/old.code/SplitMatrixByTumorType.R

In steverozen/PCAWG7: Repository of Data from paper 'The repertoire of Mutational Signatures in Human Cancer'

#' Split an exposure matrix or spectrum matrix into a list of matrices, each for a single tumor type.
#'
#' @param M A numerical matrix or data frame in which
#'   columns are samples (e.g. tumors) and rows are either
#'   mutational signatures (for exposures) or mutation types (for
#'   spectra), and, each element is the number of mutations due
#'   to a given mutational
#'   signature or mutation type in a single sample.
#'
#' @param sample.type A character or numeric vector, each element
#'   of which indicates a particular sample type.
#'
#' @return Invisibly, the list of exposure matrices created by splitting
#'   \code{M} by \code{sample.type}.
#'
#' @export
#'
SplitMatrixBySampleType <- function(M, sample.type) {
  tt <- t(M)
  split.tt <- split(as.data.frame(tt), sample.type)
  rr <- lapply(split.tt, t)
  invisible(return(rr))
}

#' Extract tumor type from column names and return the input matrix split by tumor type.
#'
#' @return Invisibly, the list of exposure matrices created by splitting
#'   \code{matrix} by the tumor type encoded in the column names.
#'
#' @export
#'
SplitPCAWGMatrixByTumorType <- function(M) {
  tumor.type <-  PCAWG7::SampleIDToCancerType(colnames(M))
  invisible(return(SplitMatrixBySampleType(M, tumor.type)))
}