determineSynonymous: Determine whether or not variants are synonomous

Description

From a table of variants, determine whether each is synonymous or non-synonomous, assuming all are in the coding region.

Usage

determineSynonymous(varTable, seqIDcol = 1, refPosCol = "Reference.Position", refAlleleCol = "Reference", varAlleleCol = "Allele", readCutoffs = 1, colprepend = "snvs_", codonStartPos = "cds", referenceSeqs)

Arguments

varTable

A data.frame with rows for each position in each gene with a variant present. Columns give various information for each included individual. This is expecting the format from readVariantFiles, which should be easy to emulate

seqIDcol

Which column is the sequence ID in? Can be numeric or character.

refPosCol

Which column is the referencece position in? Can be numeric or character.

refAlleleCol

Which column has the reference allele? Can be numeric or character.

varAlleleCol

Which column has the variable alleles? Can be numeric or character.

readCutoffs

How many variable positions need to be present to calculate bias. Set to 1 (or 0 or NULL) to include all. Without a reference, small numbers will be almost meaningless.

colprepend

What name should the output columns be prepended with.

codonStartPos

If "cds" assumes all start at position 1 (default). In the future, can be a vector giving which position each gene starts at; currently not handled.

referenceSeqs

List of FASTA sequences, with names being gene names as listed in seqIDcol and containing the sequences. This is the format produced by read.fasta, but can be emulated.

Value

variantInfo: A matrix of info for each variant, including the reference and variant values for allele and amino acid, and whether or not is synonomous
geneInfo: A matrix of info for each gene, with number and proportion for both synonymous and non-synonomous variants for the gene.

Examples

Run this code


## Load needed data
data(varScanExample)
data(fastaExample)

determineSynonymous(varTable=varScanExample,
                    refPosCol=2,
                    refAlleleCol="Ref",
                    varAlleleCol="Var",
                    referenceSeqs=fastaExample)

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