snpgdsIndInb: Individual Inbreeding Coefficients

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

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"), allele.freq=NULL,
	out.num.iter=TRUE, reltol=.Machine$double.eps^0.75, verbose=TRUE)

Arguments

gdsobj	a GDS file object (gds.class)
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
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.

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.