#' Retrieves built-in reference mutation signature sets
#'
#' Built in mutation signature sets provide reference data for
#' the analysis of N-of-1 mutation catalogs. This function provides
#' an interface for loading these reference datasets.
#'
#' @param signature_set The name of the reference signature dataset.
#' currently available options:
#' cosmic_30 (default) - the WTSI 30 SNV signatures
#' cosmic_30_exome - WTSI signatures adjusted for exome trinucleotide frequencies
#' nikzainal_sv - Structural variant signature frequencies
#'
#' @return Data frame containing reference signatures in wide format, with a mutation_type column
#'
#' @import dplyr
#'
#' @export
get_reference_signatures <- function(signature_set = 'cosmic_30') {
available_reference_sets <- c(
'cosmic_30',
'cosmic_30_exome',
'nikzainal_sv'
)
if (! signature_set %in% available_reference_sets) {
stop(sprintf('Signature set %s is not available', signature_set))
}
has_data <- function(x) { sum(!is.na(x)) > 0 }
if (signature_set == 'cosmic_30') {
data('wtsi_30_snv_signatures')
wtsi_30_snv_signatures %>%
arrange(mutation_type)
} else if (signature_set == 'cosmic_30_exome') {
data('wtsi_30_snv_signatures_exome')
wtsi_30_snv_signatures_exome %>%
arrange(mutation_type)
} else if (signature_set == 'nikzainal_sv') {
data('nikzainal_sv_signatures')
nikzainal_sv_signatures %>%
arrange(mutation_type)
}
}
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