predictSpliced {SGSeq} | R Documentation

## Ranges-based identification of splice junctions and exons

### Description

Ranges-based identification of splice junctions and exons.

### Usage

    predictSpliced(frag_exonic, frag_intron, min_junction_count, psi, beta, gamma,
      min_anchor, include_counts, retain_coverage, junctions_only, max_complexity,
      sample_name, seqlevel, strand)

### 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
`beta` | Minimum relative coverage required for an internal exon to be included
`gamma` | Minimum relative coverage required for a terminal exon to be included
`min_anchor` | Integer specifiying minimum anchor length
`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.
`junctions_only` | Logical indicating whether predictions should be limited to identification of splice junctions only
`max_complexity` | Maximum allowed complexity. If a locus exceeds this threshold, it is skipped, resulting in a warning. Complexity is defined as the maximum number of unique predicted splice junctions overlapping a given position. High complexity regions are often due to spurious read alignments and can slow down processing. To disable this filter, set to `NA`.
`sample_name` | Sample name used in messages
`seqlevel` | `seqlevel` to be processed
`strand` | `strand` to be processed

### Value

`IRanges` with predicted features

### Author(s)

Leonard Goldstein

[Package SGSeq version 1.21.9 Index]