PopGenome (version 2.1.6)

get.codons-methods: 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

## S3 method for class 'GENOME':
get.codons(object, regionID)

Arguments

object

an object of class "GENOME"

regionID

what region/alignment should be analyzed ?

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

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.

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)