seq_gtf {polyester} | R Documentation |
Given a GTF file (for transcript structure) and DNA sequences, return a DNAStringSet of transcript sequences
seq_gtf(gtf, seqs, feature = "transcript", exononly = TRUE, idfield = "transcript_id", attrsep = "; ")
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 ( |
feature |
one of |
exononly |
if |
idfield |
in the |
attrsep |
in the |
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).
http://www.ensembl.org/info/website/upload/gff.html
## 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)