Fis: Calculates allele and genotype frequencies

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/Fis.R

Description

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

Usage

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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, <[email protected]>

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

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

Demerelate documentation built on May 30, 2017, 8:14 a.m.