DNAtoAA: DNA Codon to Amino Acid Peptide Conversion routines

Description Usage Arguments Details Value See Also Examples

View source: R/codonTools.R

Description

Convert DNA sequences to amino acid peptides, in 1 or more reading frames

Usage

1
2
3
4
5
6
7
DNAtoAA(dna, clipAtStop = TRUE, readingFrames=1:6)

DNAVtoAAV(dnaVec)

DNAtoBestPeptide( dnaSet, clipAtStop = FALSE, readingFrames=1:6)

DNAtoFrameShiftingPeptides( dnaSet, min.aa.length=10)

Arguments

dna

character string of length 1, containing a sequence of nucleic acid one letter codes

dnaSet

character vector of DNA sequences

strand

coding strand that dna is from. If '-', dna will be reverse complemented before conversion

clipAtStop

should conversion stop after encountering the first stop codon

readingFrames

a vector of reading frame numbers, from 1-6, where 4-6 are the 3 reading frames on the reverse strand

dnaVec

character vector of single letter nucleic acids

min.aa.length

the shortest peptide fragment wanted returned after conversion

Details

Facilitates converting DNA sequences to amino acid sequences. The first form is moderately fast, and you choose which reading frames to use. The third form is fastest, expecting a vector of single nucleotides in frame.

All use the codon definitions table from the getCodonMap

Function DNAtoBestPeptide is a wrapper function that takes 1 or more DNA sequences, translates them in all 6 reading frames and selects the best amino acid sequence for each. Best is defined as the reading frame yielding the longest peptide with no stop codons.

Function DNAtoFrameShiftingPeptides is a wrapper function that takes 1 or more DNA sequences, assumed to be from the coding strand, and finds all suitably long protein fragments, assuming that there may be reading frame shift errors due to sequencing base caller, etc.

Value

For DNAtoAA(), a character vector of length 1 to 6, giving the amino acid sequences. The names are the read frame numbers. For DNAVtoAAV(), a character vector of single amino acids, of length length(dnaVec)/3. The stop codon is explicitly included. Invalid DNA triplets, as from 'N's, cause '?'s in the amino acid sequence.

For DNAtoBestPeptide(), a character vector of the same length as dnaSet, with the one best peptide sequence for each DNA sequence.

For DNAtoFrameShiftingPeptides(), a data frame, or a list of data frames of the same length as dnaSet, with all the sufficiently long peptide sequences and their locations, for each DNA sequence.

See Also

getCodonMap, to get the conversion table of DNA triples to amino acids. AAtoCodonOptimizedDNA, to convert from DNA to protein amino acids.

Examples

1
  DNAtoAA( "ATGAAACGGTAGANACCCGGG", clipAtStop=TRUE, readingFrames=1:6)

robertdouglasmorrison/DuffyTools documentation built on Dec. 14, 2018, 3:05 p.m.