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suchestoncampbelllab / gwasurvivr

GWAS Survival Package in R
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The reference of the HR #30

Open Ninjahelicopter opened 1 year ago

Ninjahelicopter commented 1 year ago

Hi!! Rcently I applied plinkCoxSurv function to plink bed format for survival analysis and I have two questions:

1.In the output there are "A0","A1", and "HR" and so on. So was the HRs calculated taking reference A0 or A1? 2.In the example output impute_example.coxph, it seems that A0 is REF while A1 is ALT. But when I applied plinkCoxSurv, it seems the other way around. Then, is A0 or A1 the REF?

Thank you very much.

oghzzang commented 1 year ago

I think you need to use the following option: flip.dosage=FALSE

It worked for me.!!

Ninjahelicopter commented 1 year ago

I think you need to use the following option: flip.dosage=FALSE

It worked for me.!!

Thanks. Do you know the "HRs" generated in the results take A0 or A1 as reference then?

oghzzang commented 1 year ago

Hi, When I use "flip.dosage=TRUE", it used the count of A1 allele. However when I use "flip.dosage=FALSE", they used the count of A0 allele.

And I'll check it again.

Ninjahelicopter commented 1 year ago

Later I checked myself it seems A1 is the effect allele in the output. Let me know what you think! Thanks.

Its a pitty that it's not specified in the manual.

aarizvi commented 1 year ago

Later I checked myself it seems A1 is the effect allele in the output. Let me know what you think! Thanks.

Its a pitty that it's not specified in the manual.

More than welcome to submit a pull request.