seq_gtf {polyester} | R Documentation

## Get transcript sequences from GTF file and sequence info

### Description

Given a GTF file (for transcript structure) and DNA sequences, return a DNAStringSet of transcript sequences

### Usage

    seq_gtf(gtf, seqs, feature = "transcript", exononly = TRUE,
      idfield = "transcript_id", attrsep = "; ")

### Arguments

`gtf` | one of path to GTF file, or data frame representing a canonical GTF file.
`seqs` | one of path to folder containing one FASTA file (`.fa` extension) for each chromosome in `gtf`, or named DNAStringSet containing one DNAString per chromosome in `gtf`, representing its sequence. In the latter case, `names(seqs)` should contain the same entries as the `seqnames` (first) column of `gtf`.
`feature` | one of `'transcript'` or `'exon'` (default transcript), depending on desired return.
`exononly` | if `TRUE` (as it is by default), only create transcript sequences from the features labeled `exon` in `gtf`.
`idfield` | in the `attributes` column of `gtf`, what is the name of the field identifying transcripts? Should be character. Default `"transcript_id"`.
`attrsep` | in the `attributes` column of `gtf`, how are attributes separated? Default `"; "`.

### Value

If feature is `'transcript'`, DNAStringSet containing transcript sequences, with names corresponding to `idfield` in `gtf`. If feature is `'exon'`, DNAStringSet containing exon sequences from `gtf`, named by exon location (chr, start, end, strand).

### References

http://www.ensembl.org/info/website/upload/gff.html

### Examples

     ## Not run:
      library(Biostrings)
      system('wget https://www.dropbox.com/s/04i6msi9vu2snif/chr22seq.rda')
      load('chr22seq.rda')
      data(gtf_dataframe)
      chr22_processed = seq_gtf(gtf_dataframe, chr22seq)

    ## End(Not run)

[Package polyester version 1.23.1 Index]