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#' Convert tissue specific signature exposures to reference
#'
#' This function converts tissue specific signature contributions into
#' reference signature contributions. This works on SNV signatures from SIGNAL.
#' It uses a conversion matrix to do the conversion.
#' The output can include possible artifact signatures.
#'
#' @param fit_res Named list with signature contributions and reconstructed
#' mutation matrix
#'
#' @return The input fit_res, but with converted signature contributions.
#' @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"
#' ))
#'
#' ## Get tissue specific signatures
#' signatures <- get_known_signatures(source = "SIGNAL", sig_type = "tissue", tissue_type = "Skin")
#'
#' ## Fit tissue specific signatures
#' fit_res <- fit_to_signatures(mut_mat, signatures)
#'
#' ## Convert the tissue specific signatures exposures to reference
#' fit_res <- convert_sigs_to_ref(fit_res)
convert_sigs_to_ref <- function(fit_res) {
# Get contribution
contri <- fit_res$contribution
# Determine convertion matrix filename
fname_matrix <- file.path("extdata", "signatures", "SIGNAL_conversion_matrix.txt")
fname_matrix <- system.file(fname_matrix, package = "MutationalPatterns")
# Read conversion matrix
conv_m <- read.table(fname_matrix,
sep = "\t",
header = TRUE,
stringsAsFactors = FALSE,
dec = ",",
check.names = FALSE
) %>%
tibble::column_to_rownames("Tissue_sig") %>%
as.matrix()
# Check that the tissue specific signature names are all in the conversion matrix.
if (sum(!rownames(contri) %in% rownames(conv_m))) {
stop(paste0(
"The signature names of the fit_res don't match that of ",
"the conversion matrix.\n You have to use tissue specific SNV ",
"signatures from SIGNAL."
), call. = FALSE)
}
# Remove signatures, that weren't used, from the conversion matrix.
conv_m <- conv_m[rownames(conv_m) %in% rownames(contri), , drop = FALSE]
# Convert signatures to reference.
fit_res$contribution <- t(conv_m) %*% contri
return(fit_res)
}
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