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#' Find overlap between mutations and a genomic region
#'
#' Find the number of mutations that reside in genomic region and take
#' surveyed area of genome into account.
#'
#' @param vcf CollapsedVCF object with mutations
#' @param surveyed GRanges object with regions of the genome that were surveyed
#' @param region GRanges object with genomic region(s)
#' @noRd
#' @return A data.frame containing the overlapping mutations for a
#' genomic region.
.intersect_with_region <- function(vcf, surveyed, region) {
# Number of mutations in vcf file
n_muts <- length(vcf)
# Number of base pairs that were surveyed
surveyed_length <- sum(as.numeric(BiocGenerics::width(surveyed)))
# Check if chromosome names are the same in the objects
if (GenomeInfoDb::seqlevelsStyle(vcf) != GenomeInfoDb::seqlevelsStyle(surveyed)) {
stop(paste(
"The chromosome names (seqlevels) of the VCF and the",
"surveyed GRanges object do not match."
))
}
if (GenomeInfoDb::seqlevelsStyle(region) != GenomeInfoDb::seqlevelsStyle(surveyed)) {
stop(paste(
"The chromosome names (seqlevels) of the surveyed and",
"the region GRanges object do not match."
))
}
# Intersect genomic region and surveyed region
surveyed_region <- GenomicRanges::intersect(surveyed, region, ignore.strand = TRUE)
surveyed_region_length <- sum(width(surveyed_region))
# Find which mutations lie in surveyed genomic region
overlap <- GenomicRanges::findOverlaps(vcf, surveyed_region)
muts_in_region <- as.data.frame(as.matrix(overlap))$queryHits
observed <- length(muts_in_region)
prob <- n_muts / surveyed_length
expected <- prob * surveyed_region_length
res <- data.frame(
n_muts,
surveyed_length,
prob, surveyed_region_length,
expected,
observed
)
return(res)
}
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