getSeqORFs: Extract the sequences of identified open reading frames

In rfctbio-bsu/ORFhunteR: Predict open reading frames in nucleotide sequences

Extract the sequences of identified open reading frames

Description

Extract the sequences of identified open reading frames.

Usage

getSeqORFs(orfs, tr, genome = "BSgenome.Hsapiens.UCSC.hg38", workDir = NULL)

Arguments

orfs	character string giving the name of tab-delimited TXT file with coordinates of open reading frame(-s). This file should include three mandatory fields: i) transcript_id - transcript ID; ii) start - start coordinate of open reading frame in a transcript; iii) end - end coordinate of open reading frame in a transcript.
tr	character string giving the name of file with transcript(-s) of interest. This file must include the transcript(-s) for which the open reading frame(-s) was/were identified and listed in above orfs file. Valid formats are "gtf", "gff", "fasta" and "fa".
genome	character string giving the name of BSgenome data package with full genome sequences. Default value is "BSgenome.Hsapiens.UCSC.hg38".
workDir	character string giving the path to and name of work directory. NULL by default that mean the current working directory.

Value

DNAStringSet object with sequences of extracted open reading frames.

Author(s)

Vasily V. Grinev

Examples

orfs_path <- system.file("extdata",
                         "Set.trans_ORFs.coordinates.txt",
                         package = "ORFhunteR")
tr_path <- system.file("extdata",
                       "Set.trans_sequences.fasta",
                       package = "ORFhunteR")
seq_orfs <- getSeqORFs(orfs = orfs_path,
                       tr = tr_path,
                       genome = "BSgenome.Hsapiens.UCSC.hg38",
                       workDir = NULL)

rfctbio-bsu/ORFhunteR documentation built on July 16, 2024, 10:40 a.m.