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

Description Usage Arguments Details Value References Examples

Description

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

Usage

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

## S4 method for signature '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

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 !

Value

The return value is a modified object of class "GENOME"

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The following slots will be modified in the "GENOME" object
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MKT

a matrix which includes the following values:

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

References

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

Examples

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# 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)

pievos101/PopGenome documentation built on May 16, 2019, 2:54 a.m.