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Specificy reference allele in ProbABEL modelling #5

lckarssen opened this Issue Nov 4, 2015 · 2 comments


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lckarssen commented Nov 4, 2015

This is a 'liftover' of feature request #5516 from the R-forge tracker.

Dear Yurii and Lennart,

I have a question concerning ProbABEL.

I was wondering if there is a possibility to change what is used in
the various statistical models as the predictor allele and the
reference allele, in my case for Cox regression models. I believe that
at the moment ProbABEL always uses allele A1 (as it is specified in
the info and genotypic files that are given as input/ first column in
the input files) as the predictor allele.

Is there a way to change the analysis script in such a way that the
predictor allele can be user-defined (either A1 or A2), or in a way
that ProbABEL always uses the 'minor (variant) allele' as the predictor allele?

This would be valuable in those cases where the expected number of
subjects with genotype A2A2 (the reference genotype) with an event
is zero, and several of the models (2df/dominant/recessive) are
therefore not converging. This becomes more and more frequent with
decreasing MAF of included variants. Besides, I do not know how to
deduce the effect estimate (and confidence interval) for genotype AB
vs. AA from the calculated effect estimates for AB vs. BB and AA vs. BB.

I use IMPUTE v2 imputed genotype data as input to ProbABEL, and I
cannot think of an easy way to change/swap allele coding (A/B) in
those input files. Especially if I would like to take into account the
allele frequency (to let ProbABEL select the minor allele as predictor
allele), I cannot think of a practical and easy solution. It would be
very handy if this could be specified in the statistical analysis phase.

I would greatly appreciate your help.

Thanks in advance.

Kind regards,
Anne Grotenhuis.


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lckarssen commented Jan 13, 2016

@lckarssen lckarssen self-assigned this Feb 8, 2016

@lckarssen lckarssen added this to the v0.5.0 milestone Feb 8, 2016


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lckarssen Apr 22, 2016


This issue is fixed in PR #24. The --flipmaf option will flip the reference and coding alleles in case the MAF is < 0.5.


lckarssen commented Apr 22, 2016

This issue is fixed in PR #24. The --flipmaf option will flip the reference and coding alleles in case the MAF is < 0.5.

@lckarssen lckarssen closed this Apr 22, 2016

@lckarssen lckarssen removed the in progress label Apr 22, 2016

lckarssen added a commit to lckarssen/ProbABEL that referenced this issue Dec 6, 2016

Fix memory leak (issue #31)
This fixes a memory leak introduced when implementing the `--flipmaf`
option (see Issue #5) in commit 4bbe44.
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