hom.old {GenABEL} | R Documentation |
This function computes average homozygosity (inbreeding) for a set of people, across multiple markers. Can be used for Quality Control (e.g. contamination checks)
hom.old(data, snpsubset, idsubset, weight="no")
data |
Object of gwaa.data-class or snp.data-class |
snpsubset |
Subset of SNPs to be used |
idsubset |
People for whom average homozygosity is to be computed |
weight |
When "no", homozygosity is computed as a proportion of homozygous genotypes. When "freq", an estimate of inbreeding coefficint is computed (see details). |
With "freq" option, for person i inbreeding is estimated with
f_i = \frac{O_i - E_i)}{(L_i - E_i)}
where O_i is observed homozygosity, L_i is the number of SNPs measured in individual i and
E_i = Σ_{j=1}^{L_i} (1 - 2 p_j (1 - p_j) \frac{T_{Aj}}{T_{Aj}-1})
where T_{Aj} is the numer of measured genotypes at locus j.
Only polymorphic loci with number of measured henotypes >1 are used with this option.
This measure is the same as used by PLINK (see reference).
You should use as many people and markers as possible when estimating inbreeding from marker data.
With option weight="no": A matrix with rows corresponding to the ID names and colums showing the number of genotypes measured (NoMeasured) and homozygosity (Hom).
With option weight="freq": the same as above + expected homozygosity (E(Hom)) and the estimate of inbreeding, F.
Yurii Aulchenko
Purcell S. et al, (2007) PLINK: a toolset for whole genome association and population-based linkage analyses. Am. J. Hum. Genet.
ibs
,
gwaa.data-class
,
snp.data-class
data(ge03d2) h <- hom(ge03d2[,c(1:100)]) homsem <- h[,"Hom"]*(1-h[,"Hom"])/h[,"NoMeasured"] plot(h[,"Hom"],homsem) # wrong analysis: one should use all people (for right frequency) and markers (for right F) available! h <- hom(ge03d2[,c(1:10)]) h