annotateORFs {ORFhunteR} | R Documentation

## Annotate open reading frames

### Description

Annotate the open reading frames identified in nucleotide sequences of interest.

### Usage

    annotateORFs(orfs, tr, gtf = NULL, prts, 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 format is "fasta" or "fa".
`gtf` | character string giving the name of GTF/GFF file with annotated transcripts of interest. Default value is NULL.
`prts` | character string giving the name of FASTA file with sequences of in silico translated proteins encoded by identified open reading frames.
`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 columns:

`transcript_id` | transcript ID.
`f_utr.length` | length of 5'UTRs.
`start.codon` | type of start codon.
`orf.start` | start coordinate of open reading frames.
`orf.stop` | stop coordinate of open reading frames.
`stop.codon` | type of stop codon.
`stop.status` | PTC status of stop codon.
`orf.length` | length of open reading frames.
`t_utr.length` | length of 3'UTRs.
`MW` | molecular weight.
`pI` | isoelectic point of a protein sequence.
`indexPPI` | potential protein interaction index.

### 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")
    gtf_path <- system.file("extdata",
                            "Set.trans_sequences.gtf",
                            package="ORFhunteR")
    prts_path <- system.file("extdata",
                             "Set.trans_proteins.sequences.fasta",
                             package="ORFhunteR")
    anno_orfs <- annotateORFs(orfs=orfs_path,
                              tr=tr_path,
                              gtf=gtf_path,
                              prts=prts_path,
                              workDir=NULL)

[Package ORFhunteR version 1.2.0 Index]