[R] heritability estimation

[David Winsemius]

On Oct 14, 2011, at 1:44 PM, Moohbear wrote:

> Thanks for the sos function, I didn't know about it. Unfortunately,  
> almost
> all the entries listed are not relevant to my problem.
> qgen seems to be doing what I want, but gives error message when I  
> type
> library(qgen): "Error: package 'qgen' was built before R 2.10.0:  
> please
> re-install it". I've tried and succeeded (I think) to install it  
> from the
> source, but I get the same error.
> rrBLUP should in theory do, but the I don't really understand the  
> sample
> code and it doesn't work either anyway (the sample code for  
> mixed.solve).
>
>> G <- matrix(rep(0,200*1000),200,1000)
>> for (i in 1:200) {
> + G[i,] <- ifelse(runif(1000)<0.5,-1,1)
> + }
>> u <- rnorm(1000)
>> g <- as.vector(crossprod(t(G),u))
>> h2 <- 0.5
>> y <- g + rnorm(200,mean=0,sd=sqrt((1-h2)/h2*var(g)))
>> ans <- mixed.solve(y,Z=G)
> Error in dim(x) : 'x' is missing

I'm not getting the same error with that code. I installed the binary  
rrBLUP_1.8 for Mac from a CRAN mirror with only a warning that it was  
compiled on R 2.13.2.  The copy-pasted code  runs without error on a  
slightly older version of R 2.13.1 in an even older version of my OS  
(Mac OS 10.5.8) on a three year-old machine. The next lines also run  
without error:

 > accuracy <- cor(u,ans$u)
 > accuracy
[1] 0.3117429

>
>
>
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David Winsemius, MD
West Hartford, CT