Question: logistic regression with PLINK
0
gravatar for charlie.gaoc
19 months ago by
charlie.gaoc0 wrote:

Guys, I'm running logistic regressions with plink. From the current output, I can tell the total number of individuals (case+control) from the NMISS column. My questions is, is there a way to get the number of cases and controls for each SNP as well? For example, with SNP123456, I currently know the sample size is 5,000. What's the easiest way to tell how many cases and how many controls within the 5,000 people? Greatly appreciate your help! Charlie

P.S. we dropped some genotype calls due to bad quality and we don't plan to impute the missing calls. Therefore, each SNP may have a different number of cases and controls.

logistic regression plink • 1.0k views
ADD COMMENTlink modified 19 months ago by chrchang5235.0k • written 19 months ago by charlie.gaoc0

Thanks. --freq gives nice information based on allelic information. It will be nice for me to get the numbers of individuals based on disease status/phenotype. For example, I need to know how many T2D cases and T2D controls for each SNP analyzed.

ADD REPLYlink written 19 months ago by charlie.gaoc0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 19 months ago by genomax67k
2
gravatar for chrchang523
19 months ago by
chrchang5235.0k
United States
chrchang5235.0k wrote:

With plink 1.9, "--freq case-control" stratifies the allele frequency report by disease status.

With plink 2.0, you can embed case/control allele counts directly in the logistic regression report by adding "cols=+totallelecc" after --logistic/--glm. (Note that since these are allele counts, not sample counts, the numbers will generally be twice as large.)

ADD COMMENTlink written 19 months ago by chrchang5235.0k

Thank you. I guess it's the best option I have for now. Greatly appreciate it!

ADD REPLYlink written 19 months ago by charlie.gaoc0
0
gravatar for Maxime Lamontagne
19 months ago by
Québec
Maxime Lamontagne2.1k wrote:

Maybe the "--freq" command will give you this info.

ADD COMMENTlink written 19 months ago by Maxime Lamontagne2.1k
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