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#' Count indel contexts
#'
#' @details
#' Counts the number of indels per COSMIC context from a GRanges or GRangesList object containing indel mutations.
#' This function applies the count_indel_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 indel mutations in which the context was added with get_indel_context.
#'
#' @return A tibble containing the number of indels per COSMIC context per gr.
#'
#' @examples
#' ## Get a GRangesList or GRanges object with indel contexts.
#' ## See 'indel_get_context' for more info on how to do this.
#' grl_indel_context <- readRDS(system.file("states/blood_grl_indel_context.rds",
#' package = "MutationalPatterns"
#' ))
#'
#' # Count the indel contexts
#' count_indel_contexts(grl_indel_context)
#' @family Indels
#'
#' @seealso \code{\link{get_indel_context}}
#'
#' @export
count_indel_contexts <- function(vcf_list) {
# These variables use non standard evaluation.
# To avoid R CMD check complaints we initialize them to NULL.
muttype <- muttype_sub <- NULL
categories <- INDEL_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_indel_contexts_gr, categories)
counts <- do.call(cbind, counts_l)
colnames(counts) <- names(vcf_list)
} else if (inherits(vcf_list, "GRanges")) {
counts <- .count_indel_contexts_gr(vcf_list, categories)
colnames(counts) <- "My_sample"
} else {
.not_gr_or_grl(vcf_list)
}
counts <- cbind(categories, counts)
counts[is.na(counts)] <- 0
counts <- counts %>%
tidyr::unite("muttype_total", muttype, muttype_sub) %>%
tibble::column_to_rownames("muttype_total") %>%
as.matrix()
# counts = dplyr::as_tibble(counts)
# counts$muttype = factor(counts$muttype, levels = unique(counts$muttype))
return(counts)
}
#' Count indel contexts from a single GRanges object.
#'
#' @details
#' Counts the number of indels per COSMIC context from a GRanges object containing indel mutations.
#' The function is called by count_indel_contexts
#'
#' @param gr GRanges object containing indel mutations in which the context was added with get_indel_context.
#' @param categories A tibble containing all possible indel context categories
#'
#' @return A single column tibble containing the number of indels per COSMIC context.
#'
#' @importFrom magrittr %>%
#' @noRd
#'
.count_indel_contexts_gr <- function(gr, categories) {
# These variables use non standard evaluation.
# To avoid R CMD check complaints we initialize them to NULL.
muttype <- muttype_sub <- NULL
# Check gr is not empty
if (length(gr) == 0) {
categories <- categories %>%
dplyr::mutate(count = 0) %>%
dplyr::select(-muttype, -muttype_sub)
return(categories)
}
# Check context has previously been set.
gr_colnames <- colnames(mcols(gr))
if (!all(c("muttype", "muttype_sub") %in% gr_colnames)) {
stop("The GRanges object does not contain the columns `muttype`` and `muttype_sub`.
Did you forget to run `get_indel_context`?", call. = FALSE)
}
# Classify the number of repeat units/ homopolymer length / microhomology length
# to either 5+ or 6+ depending on whether the indel is a ins or del.
id_context <- dplyr::tibble("muttype" = gr$muttype, "muttype_sub" = gr$muttype_sub) %>%
dplyr::mutate(
muttype_sub = ifelse(muttype_sub >= 6, "6+", muttype_sub),
muttype_sub = ifelse(grepl("insertion|microhomology", muttype) & muttype_sub >= 5,
"5+", muttype_sub
),
muttype_sub = as.character(muttype_sub)
) # Ensures column type for later joining
# Classify large indels as size 5+
id_context$muttype = .set_large_indels_as_5plus(id_context$muttype, gr)
id_context_count <- id_context %>%
dplyr::group_by(muttype, muttype_sub) %>%
dplyr::summarise(count = dplyr::n())
id_context_count_full <- dplyr::left_join(categories,
id_context_count,
by = c("muttype", "muttype_sub")
) %>%
dplyr::select(-muttype, -muttype_sub)
# colnames(id_context_count_full)[3] = name
return(id_context_count_full)
}
#' Classify large indels as size 5+
#' Indels with a size that is more or equal to 5,
#' are set to size 5+
#'
#' @param muttype A vector containing the contexts of the mutations
#' @param gr GRanges object containing indel mutations in which the context was added with get_indel_context.
#'
#' @return A modified version of the vector containing the contexts of the mutations
#'
#' @importFrom magrittr %>%
#' @noRd
.set_large_indels_as_5plus = function(muttype, gr){
# Determine mutation sizes
ref_sizes <- gr %>%
.get_ref() %>%
width()
alt_sizes <- gr %>%
.get_alt() %>%
unlist() %>%
width()
mut_size <- abs(alt_sizes - ref_sizes)
# Change classification of large mutations into 5+
mut_size_f <- mut_size >= 5
muttype <- ifelse(mut_size_f,
gsub("[0-9]+bp",
"5+bp",
muttype,
perl = TRUE
),
muttype
)
return(muttype)
}
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