VariantAnnotation (version 1.18.1)

getTranscriptSeqs: Get transcript sequences

Description

This function is defunct. Use GenomicFeatures::extractTranscriptSeqs() instead. Extract transcript sequences from a BSgenome object or an FaFile.

Usage

## S3 method for class 'GRangesList,BSgenome':
getTranscriptSeqs(query, subject, ...)
  ## S3 method for class 'GRangesList,FaFile':
getTranscriptSeqs(query, subject, ...)
  ## S3 method for class '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

Value

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

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).

See Also

predictCoding extractTranscriptSeqs getSeq

Examples

## See ?extractTranscriptSeqs in the GenomicFeatures package.