get.codons-methods: Detailed information about the nature of codon changes
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Usage Arguments Details Value Examples

This generic function returns some information about the codon changes resulting from the observed SNPs.

1 2	## S4 method for signature 'GENOME' get.codons(object, regionID)

`object`	an object of class `"GENOME"`
`regionID`	what region/alignment should be analyzed ?

The slot GENOME.class@region.data@synonymous and GENOME.class@region.data@codons
have to be set.
The data have to be read in with the correponding GFF file.
The function set.synnonsyn(..., save.codons=TRUE) sets the syn/nonsny
sites in case of SNP data and stores the corresponding codon changes.

The function get.codons returns a data.frame with the following information

`1`	Position of the SNPs
`2`	Major Codon
`3`	Minor Codon
`4`	Major amino acid
`5`	Minor amino acid
`6`	synonymous (TRUE/FALSE)
`7`	Polarity of the major amino acid
`8`	Polarity of the minor amino acid

# Alignments
# GENOME.class <- readData("FASTA",gffpath="GFF")
# get.codons(GENOME.class,1)
# SNP data
# GENOME.class <- readData("VCF",gffpath="GFF")
# GENOME.class <- set.synnonsyn(GENOME.class, ref.chr="ref.fas",save.codons=TRUE)
# get.codons(GENOME.class,1)