splicesiteOverlap: Compatible fragment counts for splice sites

In SGSeq: Splice event prediction and quantification from RNA-seq data

Description

Identify fragments with alignments extending across exon/intron boundaries.

Usage

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

SGSeq documentation built on Nov. 8, 2020, 8:31 p.m.