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Last data update: 2014.03.03

R: Calculates unbiased pairwise Fst between all sampled...

calculate.all.pairwise.Fst

R Documentation

Calculates unbiased pairwise Fst between all sampled populations

Description

This function calculates unbiased F_{ST} (based on Weir and Hill's θ, 2002), between all populations/individuals included in the counts matrix, and returns the results in a k by k matrix, where k = nrow(counts). Loci for which either of the populations/individuals has missing data (i.e. - the sample size is zero) are excluded.

Usage

calculate.all.pairwise.Fst(allele.counts, sample.sizes)

Arguments

`allele.counts`	A matrix of allelic count data, for which `nrow =` the number of populations and `ncol =` the number of bi-allelic loci sampled. Each cell gives the number of times allele ‘1’ is observed in each population. The choice of which allele is allele ‘1’ is arbitrary, but must be consistent across all populations at a locus.
`sample.sizes`	A matrix of sample sizes, for which `nrow =` the number of populations and `ncol =` the number of bi-allelic loci sampled (i.e. - the dimensions of `sample.sizes` must match those of `counts`). Each cell gives the number of chromosomes successfully genotyped at each locus in each population.

Value

A matrix of pairwise, unbiased F_{ST}.

Author(s)

Gideon Bradburd

References

Weir,B.S. and W.G. Hill. 2002. Estimating F-statistics. Ann.Rev.Gen. 36:949-952.

Examples

#With the HGDP dataset
	data(HGDP.bedassle.data)

#Calculate pairwise Fst between all population pairs
	hgdp.pairwise.Fst <- calculate.all.pairwise.Fst(
		HGDP.bedassle.data$allele.counts,
		HGDP.bedassle.data$sample.sizes
	)	

#Plot pairwise Fst against geographic distance
	plot(HGDP.bedassle.data$GeoDistance,
		hgdp.pairwise.Fst,
		pch=19,
		col=HGDP.bedassle.data$EcoDistance+1,
		ylab="pairwise Fst",
		xlab="geographic distance",
		main="isolation by distance")
			legend(x="bottomright",pch=19,col=c(1,2),
				legend=c("same side of Himalayas",
						"opposite sides of Himalayas"))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BEDASSLE)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BEDASSLE/calculate.all.pairwise.Fst.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calculate.all.pairwise.Fst
> ### Title: Calculates unbiased pairwise Fst between all sampled populations
> ### Aliases: calculate.all.pairwise.Fst
> 
> ### ** Examples
> 
> #With the HGDP dataset
> 	data(HGDP.bedassle.data)
> 
> #Calculate pairwise Fst between all population pairs
> 	hgdp.pairwise.Fst <- calculate.all.pairwise.Fst(
+ 		HGDP.bedassle.data$allele.counts,
+ 		HGDP.bedassle.data$sample.sizes
+ 	)	
> 
> #Plot pairwise Fst against geographic distance
> 	plot(HGDP.bedassle.data$GeoDistance,
+ 		hgdp.pairwise.Fst,
+ 		pch=19,
+ 		col=HGDP.bedassle.data$EcoDistance+1,
+ 		ylab="pairwise Fst",
+ 		xlab="geographic distance",
+ 		main="isolation by distance")
> 			legend(x="bottomright",pch=19,col=c(1,2),
+ 				legend=c("same side of Himalayas",
+ 						"opposite sides of Himalayas"))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>