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
polygenic function
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- GenABEL senior expert
- Posts: 151
- Joined: Wed Feb 09, 2011 3:24 pm
Re: polygenic function
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
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
-
- Posts: 3
- Joined: Tue Feb 07, 2012 10:00 pm
Re: polygenic function
This was written in June 2013:
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
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
Re: polygenic function
Hi
I am getting the following error:
When I run:
I double checked the phenotype file and it is in recommended order. My phenotype file has 0/1
Please help
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
Reason: Reformatted output with the [code] tag
Re: polygenic function
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
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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