processTerminalExons {SGSeq} | R Documentation

## Process predicted terminal exons

### Description

Predicted terminal exons are processed as described under Details.

### Usage

    processTerminalExons(features, min_overhang = NA)

### Arguments

`features` | `TxFeatures` object
`min_overhang` | Minimum overhang required to suppress filtering or trimming of predicted terminal exons (see Details). Use `NA` to exclude all terminal exons sharing a splice with an internal exon and trim all remaining terminal exons overlapping other exons.

### Details

Processing of terminal exon predictions is done in two steps: (1) terminal exons that share a splice site with an internal exon are filtered, and (2) remaining terminal exons that overlap other exons are trimmed.

`predictTxFeatures` predicts flanking terminal exons for each identified splice junction. This ensures that each splice junction has a flanking exon after merging with `mergeTxFeatures`. This approach results in many predicted terminal exons that share a splice site with predicted internal exons (often contained within them or with a short overhang due to incorrect alignments). Most of these are not real terminal exons and are filtered before further analysis. Filtering based on the overhang is controlled with argument `min_overhang`.

Some of the remaining predicted terminal exons overlap other exons such that their unspliced boundary shows a short overhang with respect to a spliced boundary of the overlapping exon. Often these exon extensions into an intron are due to incorrect alignments. Terminal exons with overhang smaller than `min_overhang` are trimmed such that their trimmmed unspliced boundary coincides with the spliced boundary of the overlapping exon.

### Value

`TxFeatures` object with processed features

### Author(s)

Leonard Goldstein

### Examples

    txf_processed <- processTerminalExons(txf_ann)

[Package SGSeq version 1.20.0 Index]