predictJunctions {SGSeq} | R Documentation

## Identify splice junctions

### Description

Identify splice junctions from genomic RNA-seq read alignments.

### Usage

    predictJunctions(frag_exonic, frag_intron, min_junction_count, psi, min_anchor,
      retain_coverage)

### Arguments

`frag_exonic` | `IRangesList` with exonic regions from alignments
`frag_intron` | `IRangesList` with introns implied by spliced alignments
`min_junction_count` | Minimum fragment count required for a splice junction to be included. If specified, argument `alpha` is ignored.
`psi` | Minimum splice frequency required for a splice junction to be included
`min_anchor` | Integer specifiying minimum anchor length
`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 splice junctions with metadata columns “type” and “N”, and optionally “N_splicesite” for `retain_coverage = TRUE`

### Author(s)

Leonard Goldstein

[Package SGSeq version 1.14.0 Index]