getTxsSeq {TAPseq} | R Documentation |
Extract the DNA sequences of all exons of transcript models and concatenate to one sequence per
transcript. This is basically a wrapper for extractTranscriptSeqs
,
which makes sure that the exons are correctly sorted according to their position in the
transcript (3' to 5').
getTxsSeq(transcripts, genome) ## S4 method for signature 'GRangesList' getTxsSeq(transcripts, genome) ## S4 method for signature 'GRanges' getTxsSeq(transcripts, genome)
transcripts |
A |
genome |
A |
A DNAString
or
DNAStringSet
object containing the transcript
sequence(s).
GRangesList
: Obtain transcript sequence from GRangesList
input
GRanges
: Obtain transcript sequence from GRanges
input
library(BSgenome) # protein-coding exons of transcripts within chr11 region data("chr11_genes") target_txs <- split(chr11_genes, f = chr11_genes$transcript_id) # human genome (hg38) BSgenome object (needs to be installed separately from Bioconductor) hg38 <- getBSgenome("BSgenome.Hsapiens.UCSC.hg38") # get sequences for all target transcripts on chr11 txs_seqs <- getTxsSeq(target_txs, genome = hg38)