calc.fst {fsthet} | R Documentation |
This calculates Fst.
Description
This calculates Fst. The caluclation is done as (Ht-Hs)/Ht, where Ht is the expected heterozygosity for all populations and Hs is the expected heterozygosity for each population. This calculation is used in bootstrapping functions.
Usage
calc.fst(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 |
The expected heterozygosity under Hardy-Weinberg expectations. This is a single numerical value. |
fst |
The calculated Fst value for this locus. |
Examples
gpop<-data.frame(popinfo=c(rep("POP 1", 20),rep("POP 2", 20)),ind.names=c(1:20,1:20),
loc0=sample(c("0101","0102","0202"),40,replace=TRUE))
fst1<-calc.fst(gpop,3)
## Not run:
gfile<-system.file("extdata", "example.genepop.txt",package = 'fsthet')
gpop<-my.read.gpop(gfile)
fst1<-calc.fst(gpop,3) #calculate fst for the first SNP
## End(Not run)
[Package fsthet version 1.0.1 Index]