findPTCs {ORFhunteR} | R Documentation

## 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)

[Package ORFhunteR version 1.2.0 Index]