[R-sig-ME] PedigreeMM question

[Joehanes, Roby (NIH/NHLBI) [F]]

Hi,

I would like to do something like this in pedigreemm:

result <- pedigreemm(y ~ ...<the other factors>... + (1 | id), data=mydata, pedigree=list(id=mypedigree), na.action=na.omit)

To my impression after reading pedigreemm's code, I need several observations with the same ID number and I cannot have each observation to have a different ID. Is this correct? Then, is it possible to have 1 observation having 1 ID? I don't think it is, given how the Z matrix for ID is encoded in lmer (and thereby pedigreemm) and how examples in the paper accompanying the package are constructed. Maybe I am incorrect or maybe I am doing an incorrect encoding.

What I am getting at is genome-wide association study (GWAS)-like analysis that account for familial correlation matrix. Here, each observation comes from one individual, which is associated an individual ID and a pedigree ID. One pedigree ID contains essentially a family tree from great grandparents down to the little ones. The pedigree is somewhat complicated by step-parents (indicated by siblings sharing one parent, but not the other) and a few members of one pedigree intermarrying those of another. I have the inclination to specify the model as:

result <- pedigreemm(y ~ ...<the other factors>... + (1 | ped_id), data=mydata, pedigree=list(ped_id =mypedigree), na.action=na.omit)

To me, it doesn't seem to be correct since pedigreemm will treat observations having the same ped_id as repeat observations. If I understand the code correctly, pedigreemm will tie ped_id with the mypedigree$id. I cannot put in individual IDs into mypedigree$id since it will make pedigreemm associate IDs incorrectly. However, I cannot put in pedigree ID into mypedigree$id either since one pedigree ID consists of the whole family tree.

The questions are: How can I deal with this problem? Should I break up the pedigree into nuclear families? How can I deal with the step-parents and intermarriage complications above? If pedigreemm was not designed for problems of this class, which other packages should I look into?

Thank you,
Roby