snpgdsPairIBD: Calculate Identity-By-Descent (IBD) Coefficients

In zhengxwen/SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Calculate Identity-By-Descent (IBD) Coefficients

Description

Calculate the three IBD coefficients (k0, k1, k2) for non-inbred individual pairs by Maximum Likelihood Estimation (MLE) or PLINK Method of Moment (MoM).

Usage

snpgdsPairIBD(geno1, geno2, allele.freq,
    method=c("EM", "downhill.simplex", "MoM", "Jacquard"),
    kinship.constraint=FALSE, max.niter=1000L, reltol=sqrt(.Machine$double.eps),
    coeff.correct=TRUE, out.num.iter=TRUE, verbose=TRUE)

Arguments

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
method	"EM", "downhill.simplex", "MoM" or "Jacquard", see details
kinship.constraint	if TRUE, constrict IBD coefficients ($k_0,k_1,k_2$) in the genealogical region ($2 k_0 k_1 >= k_2^2$)
max.niter	the maximum number of iterations
reltol	relative convergence tolerance; 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.
coeff.correct	TRUE by default, see details
out.num.iter	if TRUE, output the numbers of iterations
verbose	if TRUE, show information

Details

If method = "MoM", then PLINK Method of Moment without a allele-count-based correction factor is conducted. Otherwise, two numeric approaches for maximum likelihood estimation can be used: one is Expectation-Maximization (EM) algorithm, and the other is Nelder-Mead method or downhill simplex method. Generally, EM algorithm is more robust than downhill simplex method. "Jacquard" refers to the estimation of nine Jacquard's coefficients.

If coeff.correct is TRUE, the final point that is found by searching algorithm (EM or downhill simplex) is used to compare the six points (fullsib, offspring, halfsib, cousin, unrelated), since any numeric approach might not reach the maximum position after a finit number of steps. If any of these six points has a higher value of log likelihood, the final point will be replaced by the best one.

Value

Return a data.frame:

k0	IBD coefficient, the probability of sharing ZERO IBD
k1	IBD coefficient, the probability of sharing ONE IBD
loglik	the value of log likelihood
niter	the number of iterations

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.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.

See Also

snpgdsPairIBDMLELogLik, snpgdsIBDMLE, snpgdsIBDMLELogLik, snpgdsIBDMoM

Examples

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

YRI.id <- read.gdsn(index.gdsn(genofile, "sample.id"))[
    read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))=="YRI"]

# SNP pruning
set.seed(10)
snpset <- snpgdsLDpruning(genofile, sample.id=YRI.id, maf=0.05,
    missing.rate=0.05)
snpset <- unname(sample(unlist(snpset), 250))

# the number of samples
n <- 25

# specify allele frequencies
RF <- snpgdsSNPRateFreq(genofile, sample.id=YRI.id, snp.id=snpset,
    with.id=TRUE)
summary(RF$AlleleFreq)

subMLE <- snpgdsIBDMLE(genofile, sample.id=YRI.id[1:n], snp.id=RF$snp.id,
    allele.freq=RF$AlleleFreq)
subMoM <- snpgdsIBDMoM(genofile, sample.id=YRI.id[1:n], snp.id=RF$snp.id,
    allele.freq=RF$AlleleFreq)
subJac <- snpgdsIBDMLE(genofile, sample.id=YRI.id[1:n], snp.id=RF$snp.id,
    allele.freq=RF$AlleleFreq, method="Jacquard")



########################

# genotype matrix
mat <- snpgdsGetGeno(genofile, sample.id=YRI.id[1:n], snp.id=snpset,
    snpfirstdim=TRUE)

rv <- NULL
for (i in 2:n)
{
    rv <- rbind(rv, snpgdsPairIBD(mat[,1], mat[,i], RF$AlleleFreq, "EM"))
    print(snpgdsPairIBDMLELogLik(mat[,1], mat[,i], RF$AlleleFreq,
        relatedness="unrelated", verbose=TRUE))
}
rv
summary(rv$k0 - subMLE$k0[1, 2:n])
summary(rv$k1 - subMLE$k1[1, 2:n])
# ZERO

rv <- NULL
for (i in 2:n)
    rv <- rbind(rv, snpgdsPairIBD(mat[,1], mat[,i], RF$AlleleFreq, "MoM"))
rv
summary(rv$k0 - subMoM$k0[1, 2:n])
summary(rv$k1 - subMoM$k1[1, 2:n])
# ZERO

rv <- NULL
for (i in 2:n)
    rv <- rbind(rv, snpgdsPairIBD(mat[,1], mat[,i], RF$AlleleFreq, "Jacquard"))
rv
summary(rv$D1 - subJac$D1[1, 2:n])
summary(rv$D2 - subJac$D2[1, 2:n])
# ZERO

# close the genotype file
snpgdsClose(genofile)

zhengxwen/SNPRelate documentation built on Nov. 19, 2024, 1:02 p.m.