snpgdsIndInbCoef: Individual Inbreeding Coefficient

In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

Description

To calculate an individual inbreeding coefficient using SNP genotype data

Usage

snpgdsIndInbCoef(x, p, method = c("mom.weir", "mom.visscher", "mle"),
	reltol=.Machine$double.eps^0.75)

Arguments

x	SNP genotypes
p	allele frequencies
method	see details
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.

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.

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.

Examples

# open an example dataset (HapMap)
genofile <- openfn.gds(snpgdsExampleFileName())

chr1 <- read.gdsn(index.gdsn(genofile, "snp.id"))[
	read.gdsn(index.gdsn(genofile, "snp.chromosome"))==1]
chr1idx <- match(chr1, read.gdsn(index.gdsn(genofile, "snp.id")))

AF <- snpgdsSNPRateFreq(genofile)
g <- read.gdsn(index.gdsn(genofile, "genotype"), start=c(1,1), count=c(-1,1))

snpgdsIndInbCoef(g[chr1idx], AF$AlleleFreq[chr1idx], method="mom.weir")
snpgdsIndInbCoef(g[chr1idx], AF$AlleleFreq[chr1idx], method="mom.visscher")
snpgdsIndInbCoef(g[chr1idx], AF$AlleleFreq[chr1idx], method="mle")

# close the genotype file
closefn.gds(genofile)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Hint: it is suggested to call `snpgdsOpen' to open a SNP GDS file instead of `openfn.gds'.
[1] 1.837708
[1] 4.387259
[1] 0.6803821

SNPRelate documentation built on May 2, 2019, 4:56 p.m.