kaksFromVariants: Calculate Ka/Ks ratios from a table of variants

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

Description

From a table of variants, determine the ka/ks ratio and the number of synonomous/non-synonomous sites.

Usage

kaksFromVariants(varTable,
                    seqIDcol = 1,
                    refPosCol = "Reference.Position",
                    refAlleleCol = "Reference",
                    varAlleleCol = "Allele",
                    readCutoffs = 1,
                    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. Small changes to the names make it ideal for VarScan formats as well.
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.
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 matrix of info for each gene with:

ka	rate of non-synonomous subsitutions
ks	rate of synonomous subsitutions
kaks	the ka/ks ratio; Note that ka/ks will be NA for genes with no scored variants and for any gene for which ka or ks are returned as negative
nSynSites	the number of sites deemed synonomous (includes half of the two-fold synonomous sites)
nNonSynSites	the number of sites deemed non-synonomous (includes half of the two-fold synonomous sites)

Author(s)

Mark Peterson

See Also

nSynNonSites, determineSynonymous, kaks, read.fasta

Examples

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

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

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