getTranscriptSeqs-methods: Get transcript sequences

In VariantAnnotation: Annotation of Genetic Variants

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.

VariantAnnotation documentation built on Nov. 8, 2020, 5:08 p.m.