Hi,
I'm using R for a QTL analysis of SNP data. I was wondering if anyone
had any advice on fitting a dominance effect into the following
function;
> myfun4
function (x) {
x <- scan(con, nmax=169)
y <- unique(x[which(!is.na(x))])
if(length(y)>1) {
summary(lme(Ad ~ x, random= ~1|sire, na.action="na.omit"))
}
else {print("no.infomation")}
}
Con is the connection to a file of the genotypes for each SNP. It is set
up as a continues string of genotype (0, 1, 2), the first 169 for the
first SNP, the second 169 for the second SNP and so on.
I need a way of determining if the deviation of the mean of genotype 1
is significant from that of the mean of genotypes 0 & 2.
Any help would be greatly appreciated.
Cheers,
Joseph
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