splicesiteOverlap {SGSeq} | R Documentation

## Compatible fragment counts for splice sites

### 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

[Package SGSeq version 1.14.0 Index]