PopGenome (version 1.2.6)

MKT-methods: McDonald-Kreitman Test (McDonald & Kreitman 1991)

Description

This generic function calculates an approximate version of the McDonald-Kreitman Test.

Usage

## S3 method for class 'GENOME':
MKT(object,new.populations=FALSE)
## S3 method for class 'GENOME':
get.MKT(object)

Arguments

object

an object of class "GENOME"

new.populations

list of populations. default:FALSE

Value

• Returned value is an modified object of class "GENOME" --------------------------------------------------------- Following slots will be modified in the "GENOME" object ---------------------------------------------------------
• MKT
  a matrix which includes following values:
• rll{ Columns Description 1. P_nonsyn nonsynonymous sites 2. P_syn synonymous sites 3. D_nonsyn fixed nonsynonymous sites 4. D_syn fixed synonymous sites 5. neutrality.index $(P_{nonsyn}/P_{syn})/(D_{nonsyn}/D_{syn})$ 6. alpha 1-neutrality.index }

Details

This function assumes that in population genetic analysis the probability of two variants in one codon is very small. Due to this only single nucleotide polymorphisms (SNPs) are examined. When there was no gff-file specified, an alignment in the right reading frame is expected. The outgroup has to be defined as a population !

References

McDonald, J. H.; Kreitman, M. (1991). Adaptive protein evolution at the Adh locus in Drosophila. Nature 351 (6328): 652-654

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- MKT(GENOME.class)
# GENOME.class <- MKT(GENOME.class,list(1:7,8:12))
# show the result:
# get.MKT(GENOME.class)