PopGenome (version 1.2.6)

get.codons-methods: Detail informations about codon-substitutions

Description

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

Usage

## S3 method for class 'GENOME':
get.codons(object, regionID, reading.start.pos, ref.chr)

Arguments

object

an object of class "GENOME"

regionID

what region should be analyzed ?

reading.start.pos

start position of the reading frame

ref.chr

reference chromosome as a FASTA-file

Value

• The function get.codons returns a data.frame with following informations,
• 1
  Position of the SNPs
• 2
  Mayor Codon
• 3
  Minor Codon
• 4
  Mayor Protein
• 5
  Minor Protein
• 6
  synonymous (TRUE/FALSE)
• 7
  Polarity of the Mayor Protein
• 8
  Polarity of the Minor Protein

Examples

# GENOME.class <- readSNP("MPI",CHR=1)
# GENOME.class.split <- splitting.data(GENOME.class,positions=list(10000:20000),type=2)
# get.codons(GENOME.class.split,1,1000,"chromosome1.fas")