PopGenome (version 2.7.5)

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

Description

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

Usage

# S4 method for GENOME
MKT(object,
new.populations=FALSE,
do.fisher.test=FALSE,
fixed.threshold.fst=FALSE,
subsites=FALSE)
# S4 method for GENOME
get.MKT(object)

Arguments

object

an object of class "GENOME"

new.populations

list of populations. default:FALSE

do.fisher.test

P-value calculation out of the Dn,Ds,Pn,Ps table

fixed.threshold.fst

Fixed threshold

subsites

Subsites

Value

The return value is a modified object of class "GENOME" --------------------------------------------------------- The following slots will be modified in the "GENOME" object ---------------------------------------------------------

MKT

a matrix which includes the 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 approximate version of the McDonald-Kreitman test assumes that the probability that two single nucleotide polymorphisms (SNPs) occur in the same codon is very small. Thus, only codons with a single SNP are examined. If no gff-file was specified when the data was read in, it is assumed that the alignment is in the correct reading frame (starting at a first codon position). 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

# NOT RUN {
# 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)
# }