determineSynonymous: Determine whether or not variants are synonomous

In rnaseqWrapper: Wrapper for several R packages and scripts to automate RNA-seq analysis

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

Returns a list with:

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.

Author(s)

Mark Peterson

See Also

read.fasta, nSynNonSites, kaksFromVariants

Examples

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

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

rnaseqWrapper documentation built on May 2, 2019, 5:58 a.m.