getTxsSeq {TAPseq} | R Documentation

## Get transcript sequences

### Description

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').

### Usage

    getTxsSeq(transcripts, genome)

    ## S4 method for signature 'GRangesList'
    getTxsSeq(transcripts, genome)

    ## S4 method for signature 'GRanges'
    getTxsSeq(transcripts, genome)

### Arguments

`transcripts` | A `GRanges` or `GRangesList` object containing exons of transcripts for which sequences should be extracted. All exons in a `GRanges` object are assumed to belong to the same transcript. Multiple transcripts can be provided in a `GRangesList` object.
`genome` | A `BSgenome` or `DNAStringSet` object containing chromosome sequences which should be used to extract transcript sequences. Although using a `BSgenome` object is the easiest way, the genome sequence could also be loaded from a FASTA file using `readDNAStringSet`.

### Value

A `DNAString` or `DNAStringSet` object containing the transcript sequence(s).

### Methods (by class)

- `GRangesList`: Obtain transcript sequence from `GRangesList` input

- `GRanges`: Obtain transcript sequence from `GRanges` input

### Examples

    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)

[Package TAPseq version 0.99.6 Index]