TxFeatures {SGSeq} | R Documentation

## Transcript features

### Description

Creates an instance of S4 class `TxFeatures` for storing transcript features.

### Usage

    TxFeatures(x, type = mcols(x)$type, txName = mcols(x)$txName,
      geneName = mcols(x)$geneName)

### Arguments

`x` | `GRanges` with known strand (“+”, “-”)
`type` | Character vector or factor, taking value `J`, `I`, `F`, `L`, or `U`
`txName` | `CharacterList` of transcript names or `NULL`
`geneName` | `CharacterList` of gene names or `NULL`

### Details

`TxFeatures` extends `GRanges` with column slot `type` specifying feature type. `type` is a factor with levels `J` (splice junction), `I` (internal exon), `F` (5' terminal exon), `L` (3' terminal exon), `U` (unspliced transcript).

`txName` and `geneName` are CharacterLists storing transcript and gene annotation, respectively.

### Value

`TxFeatures` object

### Author(s)

Leonard Goldstein

### Examples

    gr <- GRanges(1, IRanges(101, 200), "+")
    txf <- TxFeatures(gr, type = "J")

[Package SGSeq version 1.28.0 Index]