Question: Permutations of GWAS for GWASTools
0
gravatar for chintanm
4.0 years ago by
chintanm0
United States
chintanm0 wrote:

I want to permutation tests of the full GWAS using "GWASTools". In each permutation, responses are randomly permuted and I am interested in obtaining the p-value for each test of total genomic effect. Since the MAF and other stats are fixed, evaluating them in the permutations is unnecessary. Can I speed up the "assocRegression" function so that it only evaluates the p-value for each test?

Thank you.

gwastools • 930 views
ADD COMMENTlink modified 4.0 years ago by Stephanie M. Gogarten670 • written 4.0 years ago by chintanm0
Answer: Permutations of GWAS for GWASTools
0
gravatar for Stephanie M. Gogarten
4.0 years ago by
University of Washington
Stephanie M. Gogarten670 wrote:

There is no way to turn off computing the MAF, but I don't think you would see much of a time difference regardless. The MAF calculation is very fast compared with running the regression for each SNP. I'm not sure which "other stats" you're referring to, but they either take a negligible amount of time (EAF, n) or will change with each permutation (Est, SE, etc.)

ADD COMMENTlink written 4.0 years ago by Stephanie M. Gogarten670

Thank you for the prompt reply!

ADD REPLYlink written 4.0 years ago by chintanm0
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