Coxph interactions not working (interaction parameter out of [SOLVED]

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ehillburns
Posts: 2
Joined: Thu Oct 08, 2015 2:02 pm

Coxph interactions not working (interaction parameter out of [SOLVED]

Postby ehillburns » Thu Oct 08, 2015 5:43 pm

We are having problems running pacoxph with interactions (these issues seem somewhat similar to a couple of recent posts about pacoxph problems).

When our phenotype file includes four columns (ID, Age, Event, cov1) and the interaction parameter is specified as interaction==1, the model given is incorrect (Coxph model: ( Age , Event ) ~ mu + cov1 + SNP_A1 + mu*SNP_A1).

When the interaction parameter is specified as interaction==2, the model shown is now correct, Coxph model: ( Age , Event ) ~ mu + cov1 + SNP_A1 + cov1*SNP_A1, but the analysis doesn't run, giving the following error
error: Interaction parameter is out of range (interaction=2)

When we include a phenotype file with an additional covariate column (ID, Age, Event, cov1, cov2) and specify interaction==2, the model looks ok (with the exception of a covariate we didn't want to include), Coxph model: ( Age , Event ) ~ mu + cov1 + cov2 + SNP_A1 + cov1*SNP_A1, and the analysis seems to run, but it's not clear what analysis is being run to give the results; we can't replicate any of the results shown in R.

Any suggestions?

lckarssen
Site Admin
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Location: Utrecht, The Netherlands

Re: Coxph interactions not working (interaction parameter ou

Postby lckarssen » Wed Oct 14, 2015 10:23 am

Which version of ProbABEL/pacoxph are you using?
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Lennart Karssen
PolyOmica
The Netherlands
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ehillburns
Posts: 2
Joined: Thu Oct 08, 2015 2:02 pm

Re: Coxph interactions not working (interaction parameter ou

Postby ehillburns » Wed Oct 14, 2015 12:51 pm

We're using probabel v. 0.4.5

lckarssen
Site Admin
Site Admin
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Joined: Tue Jan 04, 2011 3:04 pm
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Re: Coxph interactions not working (interaction parameter ou

Postby lckarssen » Wed Oct 14, 2015 8:11 pm

Aha, that's indeed the latest version.

We have been fixing some of the interaction code in 0.4.5, so I'm surprised this pops up (see bugs #6010 and #5883.

I have created a new bug #6194 for this issue. My time for ProbABEL maintenance is quite limited, currently, so I'm not sure when I can have a look at this.
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Lennart Karssen
PolyOmica
The Netherlands
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lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: Coxph interactions not working (interaction parameter out of

Postby lckarssen » Fri Apr 22, 2016 9:03 pm

This problem should be fixed in pull request #26 on Github which will be part of the next ProbABEL release.
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Lennart Karssen
PolyOmica
The Netherlands
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