get.codons-methods: Detailed information about the nature of codon changes

Description Usage Arguments Details Value Examples

Description

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

Usage

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

Arguments

object

an object of class "GENOME"

regionID

what region/alignment should be analyzed ?

Details

The slot [email protected]@synonymous and [email protected]@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.

Value

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

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Position of the SNPs

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Major Codon

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Minor Codon

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Major amino acid

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Minor amino acid

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synonymous (TRUE/FALSE)

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Polarity of the major amino acid

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Polarity of the minor amino acid

Examples

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# 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)

PopGenome documentation built on May 20, 2018, 5:03 p.m.