[R] Dominance in qtl model

[Charles C. Berry]

On Mon, 23 Apr 2007, joseph powell (RI) wrote:

> 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")}
> }
>

Use

 	Ad ~ x + I( 1 - abs( x - 1 ) )

in place of

 	Ad ~ x

>
> 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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Charles C. Berry                        (858) 534-2098
                                          Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	         UC San Diego
http://biostat.ucsd.edu/~cberry/         La Jolla, San Diego 92093-0901