fst.boot.onecol: This bootstraps across all individuals to calculate a...

In fsthet: Fst-Heterozygosity Smoothed Quantiles

Description

This calculates Fst using calc.fst. It randomly selects a column containing genotype information for all individuals. It then calculates Fst and Ht for that locus.

Usage

fst.boot.onecol(df, fst.choice)

Arguments

df	A dataframe containing the genepop information, where the first column is the population ID.
fst.choice	A character defining which fst calculation is to be used. The three options are: Wright's Fst (Wright, wright, WRIGHT, W, w) Weir and Cockerham 1993's beta (WeirCockerham,weircockerham,wc,WC) Corrected Weir and Cockerham 1993's beta from Beaumont and Nichols 1996 (WeirCockerhamCorrected, weircockerhamcorrected,corrected,wcc,WCC)

Value

ht.fst

A vector containin Ht and Fst

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)
   }
   fsts<-calc.actual.fst(gpop)
  nloci<-(ncol(gpop)-2)
  boot.out<-as.data.frame(t(replicate(nloci, fst.boot.onecol(gpop,"fst"))))
## Not run: 
  gfile<-system.file("extdata", "example.genepop.txt",package = 'fsthet')
  gpop<-my.read.genepop(gfile)
  fsts<-calc.actual.fst(gpop)
  nloci<-(ncol(gpop)-2)
  boot.out<-as.data.frame(t(replicate(nloci, fst.boot.onecol(gpop,"fst"))))
  outliers<-find.outliers(fsts,boot.out)

## End(Not run)

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