Hello,
I use glm within a function testing for the appearence of the coexistence
of (minor allels in a subset of) snps. And then I extract the
Pr(>|z|)-value for the interaction. Principally it works but sometimes the
function stops because this "value for the interaction" is NA. For
instance, this is the case in the following example:
lz <- glm(trait~rs7572685*rs10520302, data=mus, family=binomial)
> summary (lz)
...
Coefficients: (1 not defined because of singularities)
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.05614 0.16782 0.335 0.738
rs7572685 0.49041 0.41437 1.183 0.237
rs10520302 0.49269 0.43514 1.132 0.258
rs7572685:rs10520302 NA NA NA NA
...
I would prefer some values instead of NA (though it does not make any sense
in terms of interpretation) for the sake of the smooth running of my
function. How is this done? I guess I have to change the offset but I dont
understand how.
Thanks
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