SGSeq (version 1.2.2)

convertToSGFeatures: Convert transcript features to splice graph features

Description

Convert transcript features (predicted from RNA-seq data or extracted from transcript annotation) to splice graph features.

Usage

convertToSGFeatures(x, coerce = FALSE)

Arguments

x

TxFeatures object

coerce

Logical indicating whether transcript features should be coerced to splice graph features without disjoining exons and omitting splice donor and acceptor sites

Value

An SGFeatures object

Details

Splice junctions are unaltered. Exons are disjoined into non-overlapping exon bins. Adjacent exon bins without a splice site at the shared boundary are merged.

Entries for splice donor and acceptor sites (positions immediately upstream and downstream of introns, respectively) are added.

In the returned SGFeatures object, column type takes values “J” (splice junction), “E” (exon bin), “D” (splice donor) or “A” (splice acceptor). Columns splice5p and splice3p indicate mandatory splices at the 5' and 3' end of exon bins, respectively (determining whether reads overlapping exon boundaries must be spliced at the boundary to be considered compatible). splice5p (splice3p) is TRUE if the first (last) position of the exon coincides with a splice acceptor (donor) and it is not adjacent to a neighboring exon bin.

Each feature is assigned a unique feature and gene identifier, stored in columns featureID and geneID, respectively. The latter indicates features that belong to the same gene, represented by a connected component in the splice graph.

Examples

sgf <- convertToSGFeatures(txf)