getSeqORFs {ORFhunteR} | R Documentation

## 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)

[Package ORFhunteR version 1.2.0 Index]