calc.betahat: This calculates beta-hat, the Fst value used in Lositan.

In fsthet: Fst-Heterozygosity Smoothed Quantiles

Description

This calculates Weir & Cockerham (1993)'s beta-hat. Beaumont & Nichols (1996) used this formulation in FDIST2 (and is implemented in Lositan) See the vignette for details on the calculation of beta.

Usage

calc.betahat(df, i)

Arguments

df	A dataframe containing the genepop information, where the first column is the population ID.
i	Column number containing genotype information.

Value

ht	HB (or 1-F1). This is a single numerical value.
fst	The calculated betahat value ((F0-F1)/(1-F1))for this locus.

Examples

   gpop<-data.frame(popinfo=c(rep("POP 1", 20),rep("POP 2", 20)),ind.names=c(1:20,1:20))
     for(i in 1:40){
      gpop[1:20,(i+2)]<-sample(c("0101","0102","0202"),20,replace=TRUE)
      gpop[21:40,(i+2)]<-sample(c("0101","0102","0202"),20,replace=TRUE)
     }
  bh<-calc.betahat(gpop, 3) #calculate betahat for the SNP
  
    gfile<-system.file("extdata", "example.genepop.txt",package = 'fsthet')
    gpop<-my.read.genepop(gfile)
    beta1<-calc.betahat(gpop,3) #calculate betahat for the first SNP
  

Example output

Parsing Genepop file...


File description:  Numerical Analysis with Nm=10, N=1000, 75 Demes, sampling 5 populations. 

...done.

fsthet documentation built on May 2, 2019, 7:55 a.m.