VariantAnnotation (version 1.14.13)

getTranscriptSeqs: Get transcript sequences

Description

DEPRECATED. Use GenomicFeatures::extractTranscriptSeqs() instead. Extract transcript sequences from a BSgenome object or an FaFile.

Usage

"getTranscriptSeqs"(query, subject, ...) "getTranscriptSeqs"(query, subject, ...) "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

## Not run: 
#   library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#   library(BSgenome.Hsapiens.UCSC.hg19)
#  
#   txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene 
#   cdsByTx <- cdsBy(txdb)
# 
#   ## Use only chromosome 20.
#   seqlevels(cdsByTx, force=TRUE) <- "chr20"
# 
#   ## Return a DNAStringSet of sequences corresponding to 
#   ## the cds regions.
#   seqs <- getTranscriptSeqs(cdsByTx, Hsapiens)
# 
#   ## Sequences for the cds regions were retrieved from the BSgenome.
#   ## Each element of the cdsByTx GRangesList is represented by
#   ## a single DNAString in 'seqs'. 
#   cdsByTx[1]
#   seqs[1]
# ## End(Not run)