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Last data update: 2014.03.03

R: Calculates unbiased pairwise Fst between a pair of...

calculate.pairwise.Fst

R Documentation

Calculates unbiased pairwise Fst between a pair of populations

Description

This function calculates unbiased F_{ST} (based on Weir and Hill's θ, 2002), between a pair of populations/individuals. Loci for which either of the populations/individuals has missing data (i.e. - the sample size is zero) are excluded.

Usage

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

Arguments

`allele.counts`	A matrix of allele counts of dimensions `nrow =` 2, one for each of the two populations/individuals between which pairwise F_{ST} is being calculated, and `ncol =` the number of loci genotyped.
`sample.sizes`	A matrix of sample sizes of dimensions `nrow =` 2, one for each of the two populations/individuals between which pairwise F_{ST} is being calculated, and `ncol =` the number of loci genotyped (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

Pairwise unbiased F_{ST} between a pair of populations/individuals

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)

#Draw 2 populations at random from the Eurasian HGDP dataset
	pop1 <- sample(nrow(HGDP.bedassle.data$allele.counts),1)
	pop2 <- sample(nrow(HGDP.bedassle.data$allele.counts),1)

#Calculate unbiased Fst between them
	pairwise.Fst <- calculate.pairwise.Fst(
		HGDP.bedassle.data$allele.counts[c(pop1,pop2),],
		HGDP.bedassle.data$sample.sizes[c(pop1,pop2),]	
	)

#Print that Fst to the console
	print(sprintf("Fst between the %s population and the %s population is %s",
		HGDP.bedassle.data$hgdp.metadata[pop1,1],
		HGDP.bedassle.data$hgdp.metadata[pop2,1],
		round(pairwise.Fst,3))
	 )

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.pairwise.Fst.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calculate.pairwise.Fst
> ### Title: Calculates unbiased pairwise Fst between a pair of populations
> ### Aliases: calculate.pairwise.Fst
> 
> ### ** Examples
> 
> #With the HGDP dataset
> 	data(HGDP.bedassle.data)
> 
> #Draw 2 populations at random from the Eurasian HGDP dataset
> 	pop1 <- sample(nrow(HGDP.bedassle.data$allele.counts),1)
> 	pop2 <- sample(nrow(HGDP.bedassle.data$allele.counts),1)
> 
> #Calculate unbiased Fst between them
> 	pairwise.Fst <- calculate.pairwise.Fst(
+ 		HGDP.bedassle.data$allele.counts[c(pop1,pop2),],
+ 		HGDP.bedassle.data$sample.sizes[c(pop1,pop2),]	
+ 	)
> 
> #Print that Fst to the console
> 	print(sprintf("Fst between the %s population and the %s population is %s",
+ 		HGDP.bedassle.data$hgdp.metadata[pop1,1],
+ 		HGDP.bedassle.data$hgdp.metadata[pop2,1],
+ 		round(pairwise.Fst,3))
+ 	 )
[1] "Fst between the Yi population and the Yi population is -0.053"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>