[R] glm - change offset to avoid NA?

[Bert Gunter]

I think what you want is

?try  ##or
?tryCatch

## The second is more flexible but slightly more complicated.

to trap the error and perhaps refit the model without interaction?

Cheers,
Bert

On Mon, Jul 15, 2013 at 10:45 AM, Hermann Norpois <hnorpois at gmail.com> wrote:
> 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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>
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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

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