[GenABEL-dev] Question on ProbABEL output

[L.C. Karssen]

Hi Wenting,

Thank you for your interest in ProbABEL. This mailing list is used for
development discussions. User support is normally done via our forum at
http://forum.genabel.org, so please use that for any follow up questions
you may have.

Having said that, see below for an answer to your question.

On 17-03-15 23:09, wenting wrote:
> Hi,
> 
> Have one question about ProbABEL output.
> I browsed the manual and didn't find definition about the "beta_SNP_add"
> column.
> 1. What's the predicted Allele in this test, is it allele1?

_add stands for additive. If you use probability files as input (with
the --ngpreds=2 option), you'll get files for other genetic models as
well (e.g. recessive and dominant), which have column names like
beta_SNP_dom.
The A1 allele is the predictor allele.

> 2. How to define this beta value.

I'm not sure what you mean with this question. In case of for example
the phenotype height and the additive genetic model, a beta of 3 for a
SNP with alleles A1=A and A2=T means that people with one copy of the T
allele (AT) are on average 3 cm (assuming height was measured in cm)
taller than people with the AA genotype. Similarly, people with TT are
in general 2×3=6cm taller. Said differently: each copy of the T allele
adds 3 cm to a person's height.

Is this what you meant with your question?


Best,

Lennart.

> 
> Thanks!
> 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
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