rnaseqWrapper (version 1.0-1)

nSynNonSites: Calculate the number of (non) synonomous sites

Description

From gene sequences, determine the number of synonomous/non-synonomous sites.

Usage

nSynNonSites(geneNames, codonStartPos = "cds", referenceSeqs)

Arguments

geneNames

A character vector or list (each with character element) giving the gene names to be analyzed.

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:

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)

See Also

determineSynonymous, kaksFromVariants, kaks, read.fasta

Examples

## Load needed data
data(fastaExample)

nSynNonSites(names(fastaExample),
             referenceSeqs=fastaExample)