convertToSGFeatures {SGSeq} | R Documentation

## 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

### 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.

### Value

`SGFeatures` object

### Author(s)

Leonard Goldstein

### Examples

    sgf <- convertToSGFeatures(txf_ann)

[Package SGSeq version 1.18.0 Index]