ASREML-R : repeated measures - QTL mapping

From: g.even <asremlforum_at_VSNI.CO.UK>
Date: Wed, 20 Jan 2010 14:41:24 +0000

Dear group,

I am trying to find the correct code in R for a qtl mapping analysis. My trait is a repeated measure with unequal numbers of observations and I am wondering if ASREML-R could fit my needs.
I am sorry if I am not very clear I am quite new in learning ASREML and animal model.
I have ~800 genotypes and around thousands of SNPs to analyse.
My individuals are supposed to be unrelated, so I don't have any pedigree file available.
Could I use ASREML-R with an "empty" pedigree file?
for example fitting my pedigree file as below :
Id Mother Father
1 0 0
2 0 0
3 0 0

Or do you know if it exists a molecular marker based method for inferring variance components that I could use in ASREML-R?
Maybe a mixte model could also fit my needs?

I try performing my analysis with the following model but I am not sure :

model.asreml <- asreml(fixed = WEIGTH ~ SNP , random = ~ide(ANIMAL,var=T,init=1) + AGE, data=myanimals, ginverse=list(ANIMAL=animal.ainv),na.method.X="omit", na.method.Y="omit")

The ANIMALS are measured for their weight 10 to 100 times during a short period (1 to 10 months).
SNP is my snp effect.


gives me the p-value for my fixed effects.

Anyway, does it could be a good strategy to begin my analysis or to I need to add a rcov term, TIME variable or other...?

Many thanks for your help


G Even

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Received on Wed Jan 20 2010 - 14:41:24 EST

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