[R] Dominance in qtl model

[joseph powell (RI)]

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