Date: 2010-12-07 21:10 Sender: Yurii AulchenkoApparently this problem may be related to a more general one. Using 'ge03d2' data set I have noticed that
library(GenABEL)
data(ge03d2)
sd(hom(ge03d2[,chromosome(ge03d2)=="1"])$F[male(ge03d2)==0])
sd(hom(ge03d2[,chromosome(ge03d2)=="2"])$F[male(ge03d2)==0])
sd(hom(ge03d2[,chromosome(ge03d2)=="3"])$F[male(ge03d2)==0])
sd(hom(ge03d2[,chromosome(ge03d2)=="X"])$F[male(ge03d2)==0])
sd for X is rather high. Is that something about how F is computed (e.g. male genotypes, while being hemizygous, are counted as 2 alleles). The trick may be that T_{Aj} is defined as 'twice the number of nonmissing genotypes for SNP j'. Should check that 'hom' indeed uses 'twice' for autosomes and whether fixing to 'once' for male X helps.
This relates to other problem -- frequencies in e.g. summary.gwaa.data are estimated under the same assumption. |