snpgdsIndInb {SNPRelate} | R Documentation

## Individual Inbreeding Coefficients

### Description

To calculate individual inbreeding coefficients using SNP genotype data

### Usage

    snpgdsIndInb(gdsobj, sample.id=NULL, snp.id=NULL,
        autosome.only=TRUE, remove.monosnp=TRUE, maf=NaN, missing.rate=NaN,
        method=c("mom.weir", "mom.visscher", "mle", "gcta1", "gcta2", "gcta3"),
        allele.freq=NULL, out.num.iter=TRUE, reltol=.Machine$double.eps^0.75,
        verbose=TRUE)

### Arguments

`gdsobj` | an object of class `SNPGDSFileClass`, a SNP GDS file
`sample.id` | a vector of sample id specifying selected samples; if NULL, all samples are used
`snp.id` | a vector of snp id specifying selected SNPs; if NULL, all SNPs are used
`autosome.only` | if `TRUE`, use autosomal SNPs only; if it is a numeric or character value, keep SNPs according to the specified chromosome
`remove.monosnp` | if TRUE, remove monomorphic SNPs
`maf` | to use the SNPs with ">= maf" only; if NaN, no MAF threshold
`missing.rate` | to use the SNPs with "<= missing.rate" only; if NaN, no missing threshold
`method` | see details
`allele.freq` | to specify the allele frequencies; if NULL, the allele frequencies are estimated from the given samples
`out.num.iter` | output the numbers of iterations
`reltol` | relative convergence tolerance used in MLE; the algorithm stops if it is unable to reduce the value of log likelihood by a factor of $reltol * (abs(log likelihood with the initial parameters) + reltol)$ at a step.
`verbose` | if TRUE, show information

### Details

The `method` can be: "mom.weir": a modified Visscher's estimator, proposed by Bruce Weir; "mom.visscher": Visscher's estimator described in Yang et al. (2010); "mle": the maximum likelihood estimation; "gcta1": F^I in GCTA, avg [(g_i - 2p_i)^2 / (2*p_i*(1-p_i)) - 1]; "gcta2": F^II in GCTA, avg [1 - g_i*(2 - g_i) / (2*p_i*(1-p_i))]; "gcta3": F^III in GCTA, the same as "mom.visscher", avg [g_i^2 - (1 + 2p_i)*g_i + 2*p_i^2] / (2*p_i*(1-p_i)).

### Value

Return estimated inbreeding coefficient.

### Author(s)

Xiuwen Zheng

### References

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.

Yang, J., Lee, S. H., Goddard, M. E. & Visscher, P. M. GCTA: a tool for genome-wide complex trait analysis. American journal of human genetics 88, 76-82 (2011).

### Examples

    # open an example dataset (HapMap)
    genofile <- snpgdsOpen(snpgdsExampleFileName())

    rv <- snpgdsIndInb(genofile, method="mom.visscher")
    head(rv$inbreeding)
    summary(rv$inbreeding)

    # close the genotype file
    snpgdsClose(genofile)

[Package SNPRelate version 1.20.1 Index]