Description Usage Arguments Value Author(s) See Also Examples
From gene sequences, determine the number of synonomous/non-synonomous sites.
1 2 3 | nSynNonSites(geneNames,
codonStartPos = "cds",
referenceSeqs)
|
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 |
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) |
Mark Peterson
determineSynonymous
,
kaksFromVariants
,
kaks
,
read.fasta
1 2 3 4 5 | ## Load needed data
data(fastaExample)
nSynNonSites(names(fastaExample),
referenceSeqs=fastaExample)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.