make.bins: This sorts Fst values into a designated number of overlapping...

In fsthet: Fst-Heterozygosity Smoothed Quantiles

Description

This breaks up Fst values into a designated number of overlapping heterozygosity bins. It returns a list containing a data.frame called bins a list called bin.fst with the Fst values for each of the Het categories.

Usage

make.bins(fsts,num.breaks=25, Ht.name="Ht", Fst.name="Fst",min.per.bin=20)

Arguments

fsts	A dataframe containing at least the columns with heterozygosity and Fst values.
num.breaks	The number of breaks used to create bins (default is 25)
Ht.name	Provide the name of the column with the heterozygosity values, unless the column is named "Ht".
Fst.name	Provide the name of the column with the Fst values, unless the column is named "Fst".
min.per.bin	If you have a smaller dataset, you can change the minimum number of loci required to be in each bin. Default is 20.

Value

list(bins,bin.fst)

A list with a data.frame called bins with the upper and lower Fst and Ht values and a list called bin.fst with the Fst values for each of the Het categories.

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"))))
  bins<-make.bins(boot.out,25,Ht.name="V1",Fst.name="V2")
  ## Not run: 
    gfile<-system.file("extdata", "example.genepop.txt",package = 'fsthet')
    gpop<-my.read.gpop(gfile)
    fsts<-calc.actual.fst(gpop)
    nloci<-(ncol(gpop)-2)
    boot.out<-as.data.frame(t(replicate(nloci, fst.boot.onecol(gpop))))
    make.bins(boot.out,25)
  
## End(Not run)

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