Compatible fragment counts for splice sites

Description

Identify fragments with alignments extending across exon/intron boundaries.

Usage

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splicesiteOverlap(splicesites, side, frag_exonic, frag_intron, min_anchor,
  include = c("all", "spliced", "unspliced"), counts = TRUE)

Arguments

splicesites

IRanges of splice sites

side

Character vector indicating whether the spliced boundary is to the left (“L”) or right (“R”) of the splice site

frag_exonic

IRangesList of exonic regions, one entry per fragment

frag_intron

IRangesList of introns, one entry per fragment

min_anchor

Integer specifiying minimum anchor length

include

Character string indicating whether considered fragments should be all that overlap the splice site (“all”), those that are spliced at the site (“spliced”) or those that are not spliced, i.e. extend into the adjacent intron (“unspliced”)

counts

Logical indicating whether counts or indices of compatible fragments should be returned

Value

Counts or list of indices of compatible fragments

Author(s)

Leonard Goldstein

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