annotateORFs: Annotate open reading frames

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

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)

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