[R-sig-ME] design matrices in MCMCglmm
Alexandre Martin
alexandre.m.martin at gmail.com
Tue Mar 31 16:07:34 CEST 2015
Hi Jarrod,
Thank you for your help.
My question is now extended to the subject of associative indirect
genetic effects.
For example in this data set :
id cage
a 1
b 2
c 1
d 1
e 2
f 2
g 2
cage is a grouping variable describing the composition of cages. For
instance, individuals a,c,d live in cage 1.
Design matrix Z_cage typically produced by MCMCglmm should be:
c1 c2
a 1 0
b 0 1
c 1 0
d 1 0
e 0 1
f 0 1
g 0 1
where phenotype of individuals {a, b, ..., g} are linked to cages 1 and 2.
Design matrix Z_mates, however, linking the phenotype of individual i to
its cage' mates is:
a b c d e f g
a 0 0 1 1 0 0 0
b 0 0 0 0 1 1 1
c 1 0 0 1 0 0 0
d 1 0 1 0 0 0 0
e 0 1 0 0 0 1 1
f 0 1 0 0 1 0 1
g 0 1 0 0 1 1 0
It is Z_cage that is given by default, whereas it is matrix Z_mates that
should be used to predict associative effects.
Is it possible to force MCMCglmm to work with Z_mates instead of Z_cage?
Thanks again!
Alexandre
Le 2015-03-28 04:01, Jarrod Hadfield a écrit :
> Hi Alexandre,
>
> The design matrices should be identical for both effects (z_{ij}=1 if
> the jth individual is the mother of individual i). The difference is in
> the correlation structure of the random effects. For environmental
> maternal effects they are assumed iid (i.e. an identity matrix) but for
> the maternal genetic effects they are assumed to be proportional to the
> A matrix. inverseA will return the inverse of A if you pass it the
> pedigree. It is this inverse that is required for forming the MME.
>
> Cheers,
>
> Jarrod
>
>
>
>
>
>
> Quoting Alexandre Martin <alexandre.m.martin at gmail.com> on Fri, 27 Mar
> 2015 16:39:40 -0400:
>
>> Dear all,
>>
>> I am working on estimating maternal effects (genetic and environmental)
>> with MCMCglmm that is new for me.
>>
>> I am trying to apply to MCMCglmm what is shown in online Muir's course
>> notes made for SAS. Leanning on Henderson’s Mixed Model Equation, these
>> notes explain how to solve MME to predict random effects “by hand”.
>>
>> Here is my concern:
>>
>> I do not know how to extract the design matrices for a MCMCglmm model,
>> e.g. the relatedness matrix or the one for maternal genetic effects. I
>> want that to understand how the design matrices are constructed by
>> comparing them to what they are supposed to look like. For instance,
>> the design matrix for maternal genetic effects should relate offspring
>> to all the individuals that are in the pedigree, whereas the design
>> matrix for maternal environmental effects should just relate offspring
>> to their mothers. Does such a difference exist when MCMCglmm constructs
>> its design matrices? If not, how to include such different matrices in
>> models?
>>
>>
>> Any help will be greatly appreciated. Thank you!
>>
>>
>> Alexandre
>>
>> [[alternative HTML version deleted]]
>>
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>
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