predictExonsTerminal {SGSeq} | R Documentation

## Identify terminal exons

### Description

Identify terminal exons based on candidate terminal exons and compatible read coverage.

### Usage

    predictExonsTerminal(candidates, frag_exonic, frag_intron, relCov, min_anchor,
      type = c("exon_L", "exon_R"), include_counts, retain_coverage)

### Arguments

`candidates` | `IRanges` of candidate internal exons
`frag_exonic` | `IRangesList` with exonic regions from alignments
`frag_intron` | `IRangesList` with introns implied by spliced alignments
`relCov` | Minimum relative coverage required for exon prediction
`min_anchor` | Integer specifiying minimum anchor length
`type` | Character string indicating whether terminal exons should be identified to the left (“exon_L”) or right (“exon_R”) of provided splice sites
`include_counts` | Logical indicating whether counts of compatible fragments should be included in metadata column “N”
`retain_coverage` | Logical indicating whether coverage for each exon should be retained as an `RleList` in metadata column “coverage”. This allows filtering of features using more stringent criteria after the initial prediction.

### Value

`IRanges` of terminal exons with metadata column “type” and optionally “N” for `include_counts = TRUE`, “N_splicesite”, “coverage” for `retain_coverage = TRUE`

### Author(s)

Leonard Goldstein

[Package SGSeq version 1.16.2 Index]