translate {bioseq.fasta} R Documentation

Do translation of the nt sequence to protein sequence

Description

Usage

translate(nt,
    table = BacterialArchaealAndPlantPlastidCode,
    bypassStop = TRUE,
    checkNt = TRUE);

Arguments

nt

The given fasta collection, which can be a single FastaSeq object, a FastaFile object, a collection of the @T:SMRUCC.genomics.SequenceModel.FASTA.FastaSeq

table

[as GeneticCodes]

bypassStop

[as boolean]

checkNt

[as boolean]

env

[as Environment]

Details

when the bypassStop parameter is TRUE and there are some invalid gene sequence that contains the stop codon symbol in the translated protein sequence, a warning message will be pushed into the R# environment message buffer.

Authors

seqtoolkit

Value

a protein FastaSeq object if the input is a single nucleotide sequence, or a FastaFile protein sequence collection if the input is a collection of the nucleotide sequence data;

this function returns a R# error message object if the input sequence data can not be cast to a nucleotide fasta sequence collection.

clr value class

Examples

[Package bioseq.fasta version 1.0.0.0 Index]