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

In pievos101/PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Detailed information about the nature of codon changes

Description

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

Usage

## 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 [e-mail]@synonymous and [e-mail]@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

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

Examples

# 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)

pievos101/PopGenome documentation built on Feb. 24, 2023, 7:11 a.m.