PopGenome (version 2.7.2)

set.synnonsyn-methods: Set synonymous positions for SNP data

Description

This generic function classifies the observed biallelic positions read from SNP data files into synonymous and non-synonymous SNPs.

Usage

# S4 method for GENOME
set.synnonsyn(object,ref.chr,save.codons=FALSE)

Arguments

object

an object of class "GENOME"

ref.chr

the reference chromosome in FASTA format

save.codons

save codon changes

Value

The return value is a modified object of class "GENOME" storing syn/nonsyn informations in the slot [e-mail]@synonymous for each SNP. (1=synonymous,0=non-synonymous) When save.codons is TRUE the SNP related codon changes are saved in the corresponding slot [e-mail]@codons. (see also get.codons(), codontable() and codonise64())

Examples

# NOT RUN {
# GENOME.class <- readData("VCF",format="VCF",gffpath="GFF.Folder")
# GENOME.class <- set.synnonsyn(GENOME.class,ref.chr="ref.fas")
# [e-mail]@synonymous 

# }