Fis: Calculates allele and genotype frequencies

In Demerelate: Functions to Calculate Relatedness on Diploid Genetic Data

Description

Internal function to prepare allele and genotype frequencies for F statistics. Rows with NA values are removed from the calculation.

Usage

Fis(tab.pop, allele.column)

Arguments

tab.pop	Object with information for one or several populations and loci. Format needs to be in accordance with inputformat.
allele.column	Loci information from column allele.column and allele.column+1 are used for the calculations.

Details

Be sure to remove all missing data in your data file. Prior to calculation of F_{is} values. Every sample containing NA values in any column will be removed. It may be better to remove complete loci columns to get good results. In any case you should check this.

Value

tab.freq	Table of allele frequencies
tab.freq.gen	Table of genotype frequencies
Homo	Sum of homozygotes
pop.size	Population size
Fis	F_{is} values calculated according to Nei 1983
Fis.weir	F_{is} values calculated according to Weir and Cockerham 1984

Author(s)

Philipp Kraemer, <[e-mail]>

References

Weir, B.S. and Cockerham, C.C. (1984) Estimating F-Statistics for the analysis of population structure. Evolution, 38, 1358-1370.
Nei, M. (1977) F-statistics and analysis of gene diversity in subdivided populations. Annals of Human Genetics, 41, 225-233.
Nei, M. and Chesser R.K. (1983) Estimation of fixation indices and gene diversities. Annals of Human Genetics, 47, 253-259.

See Also

weir Fis.calc F.stat

Examples

      ## internal function of F.stat not intended for direct use
     
     

Demerelate documentation built on May 2, 2019, 4:01 p.m.