polygenic function

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merina
Posts: 1
Joined: Wed Mar 07, 2012 12:00 pm

polygenic function

Postby merina » Thu Jun 06, 2013 7:43 pm

Hello,

Is polygenic function in GenABEL suitable for use when the random effects are correlated?
I have a phenotype in binary format. In the "trait.type" criteria two options are possible gaussian or binomial. I have used "binomial" but I don't know which link function is being used. Is there anyway to check the link function?

Thanks,

Merina

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

Re: polygenic function

Postby Nicola Pirastu » Sun Jun 09, 2013 11:39 am

Hi Merina,

to answer your question I need to ask you one first: what exactly are you trying to do?

In fact if you are only trying to run a GWAS on CC samples you can use ProbABEL, instructions can be found here on paragraph 3.2:

http://www.genabel.org/sites/default/fi ... manual.pdf

However the family option in polygenic does not really work and should not be used, if you are trying to get the coefficients of the covariates of a logistic regression you should use poligenic_hglm instead.

Hope this helps you.

Best

Nicola

Daniel E. Weeks
Posts: 3
Joined: Tue Feb 07, 2012 10:00 pm

Re: polygenic function

Postby Daniel E. Weeks » Fri Aug 14, 2015 5:05 pm

This was written in June 2013:
However the family option in polygenic does not really work and should not be used, if you are trying to get the coefficients of the covariates of a logistic regression you should use poligenic_hglm instead.


Is this statement still true?

I think it probably is, as if I try polygenic with trait.type = "binomial" with a single binary trait and no covariates, while the estimate of the mean makes sense, the subsequent FGLS check fails.

If polygenic still only works with trait.type = "gaussian", then shouldn't the trait.type = "binomial" option be removed from the polygenic code?

Thank you,
Dan Weeks

asha2015
Posts: 2
Joined: Thu Feb 04, 2016 6:33 pm

Re: polygenic function

Postby asha2015 » Thu Feb 04, 2016 6:42 pm

Hi

I am getting the following error:

Code: Select all

Error in nlm(llFUN, p = parsave, y =y,desmat = desmat, relmat =relmat,
:
non-finite value supplied by 'nlm'

When I run:

Code: Select all

model_AF <- polygenic(af ~ sex, kin=gkin, data, trait.type="binomial")

I double checked the phenotype file and it is in recommended order. My phenotype file has 0/1

Please help
Last edited by lckarssen on Thu Feb 04, 2016 10:26 pm, edited 1 time in total.
Reason: Reformatted output with the [code] tag

asha2015
Posts: 2
Joined: Thu Feb 04, 2016 6:33 pm

Re: polygenic function

Postby asha2015 » Fri Mar 18, 2016 9:15 pm

Hi

in the following code:
model_AF <- polygenic(af ~ sex, kin=gkin, data, trait.type="binomial")

Does the trait type change statistical function? I always run into an error when I choose"binomial" but "gaussian" seems to work.


Kind regards


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