compute.Fstats: Compute Fst fixation index for two populations

In cgmisc: Various functions useful in computational genetics, e.g. GWAS.

Description

Fixation index Fst is a measure of population differentiation due to genetic structure. Given a set of genotypes in two populations, the function computes fixation index Fst and corresponding indices: Fit and Fis.

Usage

  compute.Fstats(data, pops)

Arguments

data	a gwaa.data class object as used by gwaa.data-class
pops	a vector of two values indicating to which population an individual belongs

Details

• data – a standard gwaa.data-class object

• pops – a vector of two values indicating to which population an individual belongs. Typically, one uses a vector of zeroes and ones where 0 marks an individual belonging to population 1 and 1 marks an individual belonging to population 2. Often, the vector is a result of clustering in MDS-scaled genomic kinship space

Value

an fstats.result class object

Author(s)

Marcin Kierczak <[e-mail]>

References

Holsinger, Kent E.; Bruce S. Weir (2009). "Genetics in geographically structured populations: defining, estimating and interpreting FST". Nat Rev Genet 10 (9): 639-650. doi:10.1038/nrg2611. ISSN 1471-0056. PMID 19687804.

See Also

gwaa.data-class, fstats.result

Examples

## Not run: 
plot.manhattan.LD()

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cgmisc documentation built on May 2, 2019, 5:50 p.m.