| Xfix {GenABEL} | R Documentation |
Sets impossible genotypes (e.g. heterozygous male X-linked genotypes) to missing
Xfix(data)
data |
Object of gwaa.data-class |
Sets to missing genotypes in the following situations:
(1) heterozygous male X-genotypes (2) heterozygous
Y- and mtDNA genotypes (3) any Y-genotypes in females.
Should only be used after check.marker,
which identifies systematic sex errors.
The same object of gwaa.data-class, with fixed genotypes
Yurii Aulchenko
require(GenABEL.data) data(ge03d2c) # truncate the data to make the example faster ge03d2c <- ge03d2c[seq(from=1,to=nids(ge03d2c),by=2),seq(from=1,to=nsnps(ge03d2c),by=2)] # many errors mc0 <- check.marker(ge03d2c) # take only people and markers passing QC fixed0 <- ge03d2c[mc0$idok,mc0$snpok] # major errors fixed, still few males are heterozygous for X-chromsome markers mc1 <- check.marker(fixed0) # fix minor X-chromosome problems fixed1 <- Xfix(fixed0) # no errors mc2 <- check.marker(fixed1) summary(mc2)