[SOLVED] ProbABEL - pvalue

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fu-ge-la
Posts: 3
Joined: Fri Apr 01, 2011 10:38 am

[SOLVED] ProbABEL - pvalue

Postby fu-ge-la » Fri Apr 01, 2011 3:14 pm

Hello,

I was just wondering is it possible to get the pvalue in the output from the ProbABEL? And also in the pdf manual in the example of the output file the snp_z and snp_chi2 is provided but I am not getting this values in my output. Would really appreciate any help/tips with that
Last edited by fu-ge-la on Mon Apr 04, 2011 10:24 am, edited 1 time in total.

Nicola Pirastu
GenABEL senior expert
GenABEL senior expert
Posts: 151
Joined: Wed Feb 09, 2011 3:24 pm

Re: ProbABEL - pvalue

Postby Nicola Pirastu » Sun Apr 03, 2011 7:29 pm

Actually it's quite easy, basically you should use Wald test.
To compute it just do (beta/sebeta)^2. This has a chisq distribution with 1df.

In R it should look like something like:

Code: Select all


res=read.table("your_results_file",header=T,strings=F)
res$chi=(res$beta/res$sebeta)^2
res$p=pchisq(res$chi,df=1,lower=F)


And there you have your pvalues.

Hope I was clear

Nicola

fu-ge-la
Posts: 3
Joined: Fri Apr 01, 2011 10:38 am

Re: ProbABEL - pvalue

Postby fu-ge-la » Mon Apr 04, 2011 8:59 am

It definitely was. Thank you very very much :]

MariaG
GenABEL specialist
GenABEL specialist
Posts: 36
Joined: Thu Feb 03, 2011 12:29 pm

Re: [SOLVED] ProbABEL - pvalue

Postby MariaG » Fri Feb 15, 2013 4:50 pm

Dear developers

Would be really nice to have p-values calculated automatically
It was already discussed here:
http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2086&group_id=505&atid=2061

Do you plan to implement it?

best
Maria

lckarssen
Site Admin
Site Admin
Posts: 322
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: [SOLVED] ProbABEL - pvalue

Postby lckarssen » Wed Feb 27, 2013 4:07 pm

Indeed, we are working on implementing this at the moment.
Things got a little bit more complicated now that GenABEL has the Grammar-Gamma function implemented. This means that the beta's and se_beta's as calculated by ProbABEL need to be adjusted before calculating the p-value. So we will also need to add two options to the ProbABEL command line to allow people to specify these correction factors.
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Lennart Karssen
PolyOmica
The Netherlands
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