compute.fstats: Compute Fst fixation index for two populations

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

Compute Fst fixation index for two populations

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 various estimates of fixation index Fst and, for Wright's Fst, also 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

Currently, the function returns four different FST estimates (after Bhatia et al., 2014, also Holsinger et al., 2009):

• FST.naive – a na\"ive $F_ST$ estimate based on the original definition by Sewall Wright. This estimate should be treated with caution as it does not take into account statistical sampling bias.

• FST.WC – Weir and Cockerham's estimate.

• FST.Nei – Nei's estimate.

• FST.Hudson – Hudson's estimate (recommended by Bhatia et al., 2014)

NOTE! Some of the estimates may return negative values if the individuals from different populations are genetically more closely related than within each population.

Value

an fstats.result class object

Author(s)

Marcin Kierczak <[e-mail]>

References

Bhatia G, Patterson N, Sankararaman S, Price AL (2014). "Estimating and interpreting FST: The impact of rare variants". Genome Research 23: 1514-1521. 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: 
fstats  <- compute.Fstats(data, pops)

## End(Not run)

cgmisc-team/cgmisc documentation built on Jan. 3, 2024, 9:52 p.m.