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#' Pool multiple samples from a mutation matrix together
#'
#' The mutation counts of columns (samples) are added up according to the grouping variable.
#'
#' @param mut_matrix Mutation count matrix (dimensions: x mutation types
#' X n samples)
#' @param grouping Grouping variable
#'
#' @return Mutation count matrix (dimensions: x mutation types
#' X n groups)
#' @export
#' @importFrom magrittr %>%
#'
#' @examples
#' ## See the 'mut_matrix()' example for how we obtained the mutation matrix:
#' mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
#' package = "MutationalPatterns"
#' ))
#' grouping <- c(rep("colon", 3), rep("intestine", 3), rep("liver", 3))
#' pool_mut_mat(mut_mat, grouping)
pool_mut_mat <- function(mut_matrix, grouping) {
# These variables use non standard evaluation.
# To avoid R CMD check complaints we initialize them to NULL.
. <- NULL
grouping <- factor(grouping)
mut_mat_group <- mut_matrix %>%
t(.) %>%
tibble::as_tibble() %>%
dplyr::mutate(factor = grouping) %>%
dplyr::group_by(factor) %>%
dplyr::summarise_all(sum) %>%
dplyr::select(-factor) %>%
t(.)
colnames(mut_mat_group) <- levels(grouping)
return(mut_mat_group)
}
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