SGSeq (version 1.0.6)

filterTerminalExons: Filter terminal exons that share splice sites with internal exons

Description

Terminal exons that share their splice site with an internal exon are filtered based on the overhang with respect to the internal exon.

Usage

filterTerminalExons(features, min_overhang = NA, return_index = FALSE)

Arguments

features

TxFeatures object

min_overhang

For terminal exons sharing a splice site with an internal exon, minimum overhang required for terminal exon to be included. Use NA to remove all terminal exons sharing a splice site with an internal exon.

return_index

Logical indicating whether indices of retained features should be returned instead of filtered features

Value

TxFeatures object with filtered features, or indices of retained features if return_index = TRUE

Details

predictTxFeatures predicts flanking terminal exons for each identified splice junction. Thus splice junctions are guaranteed to have flanking exons, even after filtering exons during merging with mergeTxFeatures. However, many predicted terminal exons share a splice site with predicted internal exons and are often contained within them. Many of these predictions are unlikely to be real terminal exons and are excluded before further analysis.

Examples

txf_filtered <- filterTerminalExons(txf)