hom {GenABEL} | R Documentation |
This function computes average homozygosity for a set of people, across multiple markers. Can be used for Quality Control (e.g. contamination checks)
hom(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", homozygosity is computed as a sum over one minus the frequency of the homozygous allele, and then divided by the number of genotypes. |
A matrix with rows corresponding to the ID names and colums showing the number of genotypes measured (NoMeasured) and homozygosity (Hom).
Yurii Aulchenko
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)