systemPipeR (version 1.6.0)

predORF: Predict ORFs

Description

Predicts open reading frames (ORFs) and coding sequences (CDSs) in DNA sequences provided as DNAString or DNAStringSet objects.

Usage

predORF(x, n = 1, type = "grl", mode = "orf", strand = "sense", longest_disjoint=FALSE, startcodon = "ATG", stopcodon = c("TAA", "TAG", "TGA"))

Arguments

x

DNA query sequence(s) provided as DNAString or DNAStringSet object.

n

Defines the maximum number of ORFs to return for each input sequence. The ORFs identified are sorted decreasingly by their length. For instance, n=1 (default) returns the longest ORF, n=2 the two longest ones, and so on.

type

One of three options provided as character values: 'df' returns results as data.frame, while 'gr' and 'grl' (default) return them as GRanges or GRangesList objects, respectively.

mode

The setting mode='ORF' returns a continuous reading frame that begins with a start codon and ends with a stop codon. The setting mode='CDS' return continuous reading frames that do not need to begin or end with start or stop codons, respectively.

strand

One of three options passed on as character vector of length one: 'sense' performs the predictions only for the sense strand of the query sequence(s), 'antisense' does it only for the antisense strand and 'both' does it for both strands.

longest_disjoint

If set to TRUE and n='all', the results will be subsetted to non-overlapping ORF set containing longest ORF.

startcodon

Defines the start codon(s) for ORF predictions. The default is set to the standard start codon 'ATG'. Any custom set of triplet DNA sequences can be assigned here.

stopcodon

Defines the stop codon(s) for ORF predictions. The default is set to the three standard stop codons 'TAA', 'TAG' and 'TGA'. Any custom set of triplet DNA sequences can be assigned here.

Value

Returns ORF/CDS ranges identified in query sequences as GRanges or data.frame object. The type argument defines which one of them will be returned. The objects contain the following columns:

• seqnames: names of query sequences
• subject_id: identified ORF/CDS ranges numbered by query
• start/end: start and end positions of ORF/CDS ranges
• strand: strand of query sequence used for prediction
• width: length of subject range in bases
• inframe2end: frame of identified ORF/CDS relative to 3' end of query sequence. This can be important if the query sequence was extracted directly upstream of an ORF (e.g. 5' UTR upstream of main ORF). The value 1 stands for in-frame with downstream ORF, while 2 or 3 indicates a shift of one or two bases, respectively.

See Also

scaleRanges

Examples

## Load DNA sample data set from Biostrings package
file <- system.file("extdata", "someORF.fa", package="Biostrings")
dna <- readDNAStringSet(file)

## Predict longest ORF for sense strand in each query sequence
(orf <- predORF(dna[1:4], n=1, type="gr", mode="orf", strand="sense"))

## Not run: 
# ## Usage for more complex example
# library(GenomicFeatures); library(systemPipeRdata)
# gff <- system.file("extdata/annotation", "tair10.gff", package="systemPipeRdata")
# txdb <- makeTxDbFromGFF(file=gff, format="gff3", organism="Arabidopsis")
# futr <- fiveUTRsByTranscript(txdb, use.names=TRUE)
# genome <- system.file("extdata/annotation", "tair10.fasta", package="systemPipeRdata")
# dna <- extractTranscriptSeqs(FaFile(genome), futr)
# uorf <- predORF(dna, n="all", mode="orf", longest_disjoint=TRUE, strand="sense")
# grl_scaled <- scaleRanges(subject=futr, query=uorf, type="uORF", verbose=TRUE)
# export.gff3(unlist(grl_scaled), "uorf.gff")
# ## End(Not run)