Package 'ORFhunteR'

Title: Predict open reading frames in nucleotide sequences
Description: The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules from the NCBI RefSeq and Ensembl databases. The package can be used in basic and applied biomedical research related to the study of the transcriptome of normal as well as altered (for example, cancer) human cells.
Authors: Vasily V. Grinev [aut, cre] , Mikalai M. Yatskou [aut], Victor V. Skakun [aut], Maryna Chepeleva [aut] , Petr V. Nazarov [aut]
Maintainer: Vasily V. Grinev <[email protected]>
License: MIT License
Version: 1.13.0
Built: 2024-09-28 06:00:09 UTC
Source: https://github.com/bioc/ORFhunteR

Help Index

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)

Classify the pseudo and true ORF candidates derived from RNA molecules

Description

Clussify the pseudo and true ORF candidates.

Usage

classifyORFsCandidates(
  ORFLncRNAs,
  ORFmRNAs,
  pLearn = 0.75,
  nTrees = 500,
  modelRF = NULL,
  workDir = NULL,
  showAccuracy = FALSE
)

Arguments

ORFLncRNAs

the oject of the class list of non-coding pseudo ORFs.
ORFmRNAs

the oject of the class list of coding true ORFs.
pLearn

probability threshold for the "traing" class of ORFs. Default value is 0.75.
nTrees

nuber of the decision trees in randomForest. Default value is 500.
modelRF

character string giving the name of RDS-file to store the classification model. NULL by default.
workDir

character string giving the path to and name of work directory. NULL by default that mean the current working directory.
showAccuracy

logic TRUE or FALSE. Use TRUE for print accuracy metrics. Default value is FALSE

Value

The classificator object of the class randomForest.

Author(s)

Mikalai M. Yatskou

Examples

## Not run: 
clt <- classifyORFsCandidates(ORFLncRNAs, ORFmRNAs)

## End(Not run)

Identify all potential start and stop codons in a nucleotide sequence

Description

This function scans a nucleotide sequence of interest in the search of canonical start codon ATG or non-canonical start codons GTG, TTG and CTG as well as stop codons TAA, TAG and TGA.

Usage

codonStartStop(x)

Arguments

x

character string giving the nucleotide sequence.

Value

list of potential start and stop codons with their coordinates.

Author(s)

Vasily V. Grinev

Examples

codons <- codonStartStop(x = "AAAATGGCATGGTAAGTC")

Identify all variants of open reading frames in a nucleotide sequence

Description

Identify all possible variants of open reading frames in a nucleotide sequence of interest.

Usage

findORFs(x, codStart = "ATG")

Arguments

x

character string giving the nucleotide sequence of interest.
codStart

character string with type of start codon: "ATG", "GTG", "TTG" or "CTG". Default value is "ATG".

Value

matrix with start and stop positions, length and sequence of identified variants of open reading frames.

Author(s)

Vasily V. Grinev

Examples

x <- "AAAATGGCTGCGTAATGCAAAATGGCTGCGAATGCAAAATGGCTGCGAATGCCGGCACGTTGCTACGT"
orf <- findORFs(x = x, codStart = "ATG")

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)

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)

Load a set of transcripts

Description

Load a set of experimental transcripts.

Usage

loadTrExper(tr, genome = "BSgenome.Hsapiens.UCSC.hg38", workDir = NULL)

Arguments

tr

character string giving the name of file with experimental transcripts. Allowed file formats are "fasta", "fa", "gtf" or "gff".
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

List of loaded transcript sequences.

Author(s)

Vasily V. Grinev

Examples

trans <- system.file("extdata",
                     "Set.trans_sequences.fasta",
                     package = "ORFhunteR")
trans_seq <- loadTrExper(tr = trans)

Predict the true ORFs in mRNA molecules

Description

Predict the true ORFs in mRNA molecules.

Usage

predictORF(
  tr,
  genome = "BSgenome.Hsapiens.UCSC.hg38",
  model = NULL,
  prThr = 0.5,
  workDir = NULL
)

Arguments

tr

character string giving the name of file with experimental transcripts. Allowed file formats are "fasta", "fa", "gtf" or "gff".
genome

character string giving the name of BSgenome data package with full genome sequences. Default value is "BSgenome.Hsapiens.UCSC.hg38".
model

character string giving the connection or full path to the file from which the classification model is read. Use default NULL value to use our default model.
prThr

probability threshold for the "winning" class of ORFs. Default value is 0.5.
workDir

character string giving the path to and name of work directory. NULL by default that mean the current working directory.

Value

The coordinates of ORFs in mRNA molecules of interest.

Author(s)

Mikalai M. Yatskou

Examples

## Not run: 
tr_path <- system.file("extdata",
                       "Set.trans_sequences.fasta",
                       package="ORFhunteR")
model <- "http://www.sstcenter.com/download/ORFhunteR/classRFmodel_1.rds"
ORFs <- predictORF(tr=tr_path, model=model)

## End(Not run)

Translate open reading frames to proteins

Description

Translate the identified open reading frames to proteins.

Usage

translateORFs(seqORFs, aaSymbol = 1, workDir = NULL)

Arguments

seqORFs

character string giving the name of FASTA/FA file with sequences of identified open reading frames.
aaSymbol

type of amino acid symbols (one- or three-letter coding). Default value is 1.
workDir

character string giving the path to and name of work directory. NULL by default that mean the current working directory.

Value

AAStringSet object with protein sequences.

Author(s)

Vasily V. Grinev

Examples

seq_orf_path <- system.file("extdata",
                            "Set.trans_ORFs.sequences.fasta",
                            package = "ORFhunteR")
prot_seqs <- translateORFs(seqORFs = seq_orf_path)

Vectorize the ORF(-s) sequence(-s) to sequence features

Description

Vectorize the ORF(-s) sequence(-s) to sequence features.

Usage

vectorizeORFs(x)

Arguments

x

DNAStringSet object with ORF(-s) sequence(-s).

Value

The object of class data.frame with ORF(-s) vectorized into sequence features.

Author(s)

Mikalai M. Yatskou

Examples

x = DNAStringSet(x = "ATGGGCCTCA")
feats <- vectorizeORFs(x = x)