snpgdsPairIBDMLELogLik: Log likelihood for MLE method in the Identity-By-Descent...
In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

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

Calculate the log likelihood values from maximum likelihood estimation.

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snpgdsPairIBDMLELogLik(geno1, geno2, allele.freq, k0=NaN, k1=NaN,
	relatedness=c("", "self", "fullsib", "offspring", "halfsib",
	"cousin", "unrelated"), verbose=TRUE)

`geno1`	the SNP genotypes for the first individual, 0 – BB, 1 – AB, 2 – AA, other values – missing
`geno2`	the SNP genotypes for the second individual, 0 – BB, 1 – AB, 2 – AA, other values – missing
`allele.freq`	the allele frequencies
`k0`	specified IBD coefficient
`k1`	specified IBD coefficient
`relatedness`	specify a relatedness, otherwise use the values of k0 and k1
`verbose`	if TRUE, show information

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.

The value of log likelihood.

Xiuwen Zheng

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.

snpgdsPairIBD, snpgdsIBDMLE, snpgdsIBDMLELogLik, snpgdsIBDMoM

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