Get transcript sequences
getTranscriptSeqs-methods.RdThis function is defunct. Use GenomicFeatures::extractTranscriptSeqs() instead.
Extract transcript sequences from a BSgenome object or an FaFile.
Usage
# S4 method for class 'GRangesList,BSgenome'
getTranscriptSeqs(query, subject, ...)
# S4 method for class 'GRangesList,FaFile'
getTranscriptSeqs(query, subject, ...)
# S4 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
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.