convertToTxFeatures {SGSeq} | R Documentation

## Convert to TxFeatures object

### Description

Convert a `TxDb` object or a `GRangesList` of exons grouped by transcripts to a `TxFeatures` object.

### Usage

    convertToTxFeatures(x)

### Arguments

`x` | `TxDb` object or `GRangesList` of exons grouped by transcript. For import from GFF format, use function `importTranscripts`.

### Details

If `x` is a `GRangesList`, transcript names and gene names can be specified as character vectors in metadata columns `txName` and `geneName`, respectively. If missing, transcript names are based on `names(x)`. For import from GFF format, use function `importTranscripts`.

In the returned `TxFeatures` object, column `type` takes values “J” (splice junction), “I” (internal exon), “F” (5'/first exon), “L” (3'/last exon) or “U” (unspliced).

### Value

`TxFeatures` object

### Author(s)

Leonard Goldstein

### Examples

    gr <- GRanges(c(1, 1), IRanges(c(1, 201), c(100, 300)), c("+", "+"))
    grl <- split(gr, 1)
    txf <- convertToTxFeatures(grl)

[Package SGSeq version 1.18.0 Index]