pairPhiST-methods: Provides the pairwise PhiST between populations

In haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Provides the pairwise PhiST between populations

Description

This function calculates pairwise PhiST between populations using the AMOVA framework.

Usage

## S4 method for signature 'Dna'
pairPhiST(x,populations,indels="sic",nperm=99, negatives=FALSE, subset =NULL, 
showprogbar=TRUE)
## S4 method for signature 'dist'
pairPhiST(x,populations,nperm=99, negatives=FALSE, subset=NULL,showprogbar=TRUE)
## S4 method for signature 'matrix'
pairPhiST(x,populations,nperm=99,negatives=FALSE, subset=NULL,showprogbar=TRUE)

Arguments

x	an object of class Dna, "dist" or "matrix".
populations	a vector giving the populations, with one element per individual.
indels	the indel coding method to be used. This must be one of "sic", "5th" or "missing". Any unambiguous substring can be given. See distance for details.
nperm	the number of permutations. Set this to 0 to skip the permutation procedure.
negatives	boolean; if it is FALSE all negative PhiST values are replaced with zero.
subset	a vector of integers in the range [1, length(unique(populations))], only distances between selected population(s) and the rest of the populations are calculated. If it is NULL, all comparisons are done.
showprogbar	boolean; whether the progress bar is displayed or not displayed.

Details

The null distribution of pairwise PhiST under the hypothesis of no difference between the populations is obtained by permuting individuals between populations.

Value

a list with following components:

PhiST	a matrix giving the PhiST values between populations.
p	a matrix giving the p-values, or NULL if permutation test is not performed.

Methods

signature(x = "Dna")

signature(x = "dist")

signature(x = "matrix")

Note

An internal code Statphi is taken from package ade4 version 1.7-8 without any modification, author Sandrine Pavoine. Function amova from package pegas is used internally to estimate variance components, author Emmanuel Paradis.

Author(s)

Caner Aktas, [e-mail]

References

Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.

Examples

data("dna.obj")

### Method for signature 'Dna'.
x<-dna.obj
x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE]
populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2",
"pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4")

##skip permutation testing
pst<-pairPhiST(x, populations, nperm=0)
pst

##allow negative PhiST values
pst<-pairPhiST(x, populations, nperm=0, negatives=TRUE)
pst

##Gaps as missing characters.
pst<-pairPhiST(x, populations, indels="m", nperm=0, negatives=TRUE)
pst

##using subset, second population against others
pst <-pairPhiST(x, populations, nperm=0,subset=c(2))
pst


## Not run: 
## 999 permutations.
pst<-pairPhiST(x, populations, nperm=999,showprogbar=TRUE)
pst

## random populations
x<-dna.obj
populations<-sample(1:4,nrow(x),replace=TRUE)
pst<-pairPhiST(x, populations, nperm=999,showprogbar=TRUE)
pst

## populations based on clusters
x<-dna.obj
d<-distance(x)
hc<-hclust(d,method="ward.D")
populations<-cutree(hc,4)
pst<-pairPhiST(x, populations, nperm=999,showprogbar=TRUE)
pst

## End(Not run)

### Method for signature 'dist'.
x<-dna.obj
x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE]
populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2",
"pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4")
d<-distance(x)
pst<-pairPhiST(d, populations, nperm=0)
pst

### Method for signature 'matrix'.
x<-dna.obj
x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE]
populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2",
"pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4")
d<-as.matrix(distance(x))
pst<-pairPhiST(d, populations, nperm=0)
pst

haplotypes documentation built on July 26, 2023, 5:22 p.m.