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#' Count MBS variants grouped by length.
#'
#' @details
#' Counts the number of mbs grouped by length from a GRanges or GRangesList object containing mbs variants.
#' This is used, since a COSMIC context has to our knowledge not yet been defined.
#' This function applies the count_mbs_contexts_gr function to each gr in its input.
#' It then combines the results in a single tibble and returns this.
#'
#' @param vcf_list GRanges or GRangesList object containing mbs variants.
#'
#' @return A tibble containing the number of MBS per MBS length per gr.
#'
#' @examples
#' ## Get a GRangesList or GRanges object with mbs variants.
#' mbs_grl <- readRDS(system.file("states/blood_grl_mbs.rds",
#' package = "MutationalPatterns"
#' ))
#'
#' # Count the MBSs
#' count_mbs_contexts(mbs_grl)
#' @family MBS
#'
#' @export
count_mbs_contexts <- function(vcf_list) {
# These variables use non standard evaluation.
# To avoid R CMD check complaints we initialize them to NULL.
size <- NULL
categories <- MBS_CATEGORIES
# Turn grl into list if needed.
if (inherits(vcf_list, "CompressedGRangesList")) {
vcf_list <- as.list(vcf_list)
}
# Count contexts per sample
if (inherits(vcf_list, "list")) {
counts_l <- purrr::map(vcf_list, .count_mbs_contexts_gr, categories)
counts <- do.call(cbind, counts_l)
colnames(counts) <- names(vcf_list)
} else if (inherits(vcf_list, "GRanges")) {
counts <- .count_mbs_contexts_gr(vcf_list, categories)
colnames(counts) <- "My_sample"
} else {
.not_gr_or_grl(vcf_list)
}
counts <- cbind(categories, counts)
# Turn output into matrix
counts <- counts %>%
tibble::column_to_rownames("size") %>%
as.matrix()
return(counts)
}
#' Count MBS grouped by length from a single GRanges object.
#'
#' @details
#' Counts the number of MBS per MBS length from a GRanges object containing mbs variants.
#' The function is called by count_mbs_contexts
#'
#' @param gr GRanges object containing mbs variants.
#' @param categories A tibble containing all possible mbs size categories
#'
#' @return A single column tibble containing the number of MBS per MBS length
#'
#' @importFrom magrittr %>%
#' @noRd
.count_mbs_contexts_gr <- function(gr, categories) {
# These variables use non standard evaluation.
# To avoid R CMD check complaints we initialize them to NULL.
count <- size <- . <- NULL
# Create count table
counts_tb <- gr %>% # Determine different sizes
.get_ref() %>%
BiocGenerics::width() %>%
tibble::enframe(value = "size") %>%
dplyr::select(-name) %>%
dplyr::mutate(
size = ifelse(size >= 10, "10+", size),
size = as.character(size)
) %>%
dplyr::group_by(size) %>% # Count number muts per size
dplyr::summarise(count = dplyr::n(), .groups = "drop_last") %>%
dplyr::left_join(categories, ., by = "size") %>% # Add to possible categories
dplyr::mutate(count = ifelse(is.na(count), 0, count)) %>%
dplyr::select(-size)
return(counts_tb)
}
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