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joepickrell / gwas-pw

Pariwise analysis of GWAS
GNU General Public License v2.0
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variance in the effect size estimate #3

Open alessandrotestori opened 7 years ago

alessandrotestori commented 7 years ago

Hello! Does the column "variance in the effect size estimate" in the example input file refer to the standard error in an association analysis?

ZheZhang-ZZ commented 6 years ago

I also have this question. Could the developer give me a little comment about how to calculate the variance in the effect size?

ssjj791 commented 6 years ago

I noticed from the supplements in the paper in Nature Genetics 2016 (https://media.nature.com/original/nature-assets/ng/journal/v48/n7/extref/ng.3570-S1.pdf) and it said "Our method uses the Z-scores and standard errors of the estimated effect sizes for each SNP. In studies where standard errors were not provided, we approximated them using the allele frequencies from the European-descent individuals in the 1000 Genomes Phase 1 release and the reported sample size of the study (see Pickrell [2014] for details)". So it's standard error.

alessandrotestori commented 5 years ago

Thank you!