snpgdsIBDMLELogLik: Log likelihood for MLE method in the Identity-By-Descent...

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

Description

Calculate the log likelihood values from maximum likelihood estimation.

Usage

snpgdsIBDMLELogLik(gdsobj, ibdobj, k0 = NaN, k1 = NaN,
	relatedness=c("", "self", "fullsib", "offspring",
	"halfsib", "cousin", "unrelated"))

Arguments

gdsobj	a GDS file object (gds.class)
ibdobj	the snpgdsIBDClass object returned from snpgdsIBDMLE
k0	specified IBD coefficient
k1	specified IBD coefficient
relatedness	specify a relatedness, otherwise use the values of k0 and k1

Details

If (relatedness == "") and (k0 == NaN or k1 == NaN), then return the log likelihood values for each (k0, k1) stored in ibdobj. \ If (relatedness == "") and (k0 != NaN) and (k1 != NaN), then return the log likelihood values for a specific IBD coefficient (k0, k1). \ If relatedness is: "self", then k0 = 0, k1 = 0; "fullsib", then k0 = 0.25, k1 = 0.5; "offspring", then k0 = 0, k1 = 1; "halfsib", then k0 = 0.5, k1 = 0.5; "cousin", then k0 = 0.75, k1 = 0.25; "unrelated", then k0 = 1, k1 = 0.

Value

Return a n-by-n matrix of log likelihood values, where n is the number of samples.

Author(s)

Xiuwen Zheng

References

Milligan BG. 2003. Maximum-likelihood estimation of relatedness. Genetics 163:1153-1167.

Weir BS, Anderson AD, Hepler AB. 2006. Genetic relatedness analysis: modern data and new challenges. Nat Rev Genet. 7(10):771-80.

Choi Y, Wijsman EM, Weir BS. 2009. Case-control association testing in the presence of unknown relationships. Genet Epidemiol 33(8):668-78.

See Also

snpgdsIBDMLE, snpgdsIBDMoM

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