findPTCs: Identify the premature termination codons in nucleotide...

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

Identify the premature termination codons in nucleotide sequences

Description

Identify the premature termination codons in nucleotide sequences of interest.

Usage

findPTCs(orfs, gtf, 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 four 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; iv) length - length of open reading frame.
gtf	character string giving the name of GTF/GFF file with annotated transcripts of interest. Valid format is "gtf" or "gff".
workDir	character string giving the path to and name of work directory. NULL by default that mean the current working directory.

Value

data.frame object with start and stop positions, length and stop status of codons for each transcript ID.

Author(s)

Vasily V. Grinev

Examples

orfs_path <- system.file("extdata",
                         "Set.trans_ORFs.coordinates.txt",
                         package="ORFhunteR")
gtf_path <- system.file("extdata",
                        "Set.trans_sequences.gtf",
                        package="ORFhunteR")
ptcs <- findPTCs(orfs = orfs_path,
                  gtf = gtf_path,
                  workDir = NULL)

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