nSynNonSites: Calculate the number of (non) synonomous sites

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

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)

Author(s)

Mark Peterson

See Also

determineSynonymous, kaksFromVariants, kaks, read.fasta

Examples

## Load needed data
data(fastaExample)

nSynNonSites(names(fastaExample),
             referenceSeqs=fastaExample)

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