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

In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description

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

Usage

## 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

# 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)

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.