getTranscriptSeqs {VariantAnnotation} | R Documentation

## Get transcript sequences

### Description

This function is defunct. Use GenomicFeatures::extractTranscriptSeqs() instead.

Extract transcript sequences from a BSgenome object or an FaFile.

### Usage

      ## S4 method for signature 'GRangesList,BSgenome'
    getTranscriptSeqs(query, subject, ...)
      ## S4 method for signature 'GRangesList,FaFile'
    getTranscriptSeqs(query, subject, ...)
      ## S4 method for signature 'GRanges,FaFile'
    getTranscriptSeqs(query, subject, ...)

### Arguments

`query` | A GRangesList object containing exons or cds grouped by transcript.
`subject` | A BSgenome object or a FaFile from which the sequences will be taken.
`...` | Additional arguments

### Details

`getTranscriptSeqs` is a wrapper for the `extractTranscriptSeqs` and `getSeq` functions. The purpose is to allow sequence extraction from either a BSgenome or FaFile. Transcript sequences are extracted based on the boundaries of the feature provided in the `query` (i.e., either exons or cds regions).

### Value

A DNAStringSet instance containing the sequences for all transcripts specified in `query`.

### Author(s)

Valerie Obenchain

### See Also

predictCoding extractTranscriptSeqs getSeq

### Examples

    ## See ?extractTranscriptSeqs in the GenomicFeatures package.

[Package VariantAnnotation version 1.38.0 Index]