inbreedCoeff: Inbreeding coefficient
In SeqVarTools: Tools for variant data

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

Calculates the inbreeding coefficient by variant or by sample

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## S4 method for signature 'SeqVarGDSClass'
inbreedCoeff(gdsobj, margin=c("by.variant", "by.sample"), use.names=FALSE,
    parallel=FALSE)

`gdsobj`	A `SeqVarGDSClass` object with VCF data.
`margin`	Possible values are "by.variant" or "by.sample," indicating whether the calculation should be done over all samples for each variant, or over all variants for each sample.
`use.names`	A logical indicating whether to assign variant or sample IDs as names of the output vector.
`parallel`	Logical, numeric, or other value to control parallel processing; see `seqParallel` for details. Only applies if `margin="as.variant"`.

For inbreeding coefficients by variant, calculates 1 - observed heterozygosity / expected heterozygosity.

For individual inbreeding coefficients (margin="by.sample"), calculates Visscher's estimator described in Yang et al. (2010).

Values for the inbreeding coefficient.

Xiuwen Zheng, Stephanie Gogarten

Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW, Goddard ME, Visscher PM. 2010. Common SNPs explain a large proportion of the heritability for human height. Nat Genet. 42(7):565-9. Epub 2010 Jun 20.

SeqVarGDSClass, applyMethod

gds <- seqOpen(seqExampleFileName("gds"))
f <- inbreedCoeff(gds, margin="by.variant")
range(f, na.rm=TRUE)

ic <- inbreedCoeff(gds, margin="by.sample")
range(ic)
seqClose(gds)