convertGenomicBasesToCodingAA: Conversions Between DNA and AA in Chromosome or Gene Local...

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Conversions Between DNA and AA in Chromosome or Gene Local Context

Description

Functions to try to convert DNA to/from AA given a local, possibly indel modified, context.

Usage

convertGenomicBasesToCodingAminoAcids(seqID, position, end, strand = "+", 
		dnaQuery, genomeDNA, geneMap = NULL, exonMap = NULL)

convertGenomicDNAtoCodingDNA(geneID, genomeDNA = NULL)

convertAApositionToGenomicDNAposition(geneID, AAposition, AAlength)

Arguments

seqID, geneID	a single character string giving the SeqID or GeneID that is the reference location in the genome
position, end	location in reference chromosomal units of the start and stop of the DNA sequence of interest
strand	the coding strand to use, for interpreting that region of DNA
dnaQuery	the DNA sequence for that region, as called by any non-reference means, such as by a SNP/Indel caller
genomeDNA	the DNA sequence for that region, from the genomic reference
geneMap, exonMap	the current species GeneMap and ExonMap, or the relavant subset thereof, needed to interpret the DNA
AAposition, AAlength	the location and extent of the coding amino acid sequence of interest

Details

These functions try to map between DNA and AA given possibly modified genomic information, such as INDEL and SNP calling data. They are not gauranteed to work in all possible contexts! Used mostly for adding DNA to AA notation to SNP plots, etc.

Value

For convertGenomicBasesToCodingAA, a list of 3 elements. Two are character vectors of the same length as the query DNA, having empty strings and amino acid calls that represent the peptide/protein fragmant in the same physical layout as the given DNA. The third is an integer vector of amino acid ordinals giving the relative position in the final protein sequence. Insertions and/or deletions may cause elements of the query to be other than a single character.

genomic	the AA sequence of the reference genome in that region
query	the AA sequence of the query sequence in that region
aa.ordinal	the protein sequence locations of the query AA sequence in that region

For convertGenomicDNAtoCodingDNA, a character string that is the cDNA sequence for the given gene, after removing any introns and accounting for strand by possible reverse complementation.

For convertAApositionToGenomicDNAposition, a list of 2 elements:

SEQ_POSITION	the location in the genomic DNA that is the start of the first codon
SEQ_END	the location in the genomic DNA that is the end of the last codon

Note

These functions are only as valid as the underlying genome and annotation. They are not foolproof.

Author(s)

Bob Morrison

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.