Compute the corrected p-values from EIGENSTRAT chisq statistic output
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23 months ago
nastasia ▴ 10

Hello everyone,

I am working with genotype GWAS dataset which contains heterogeneous populations. I tested EIGENSTRAT software which correct for population stratification including PCA via two steps (smartpca and smarteigentrat).

The output file contains chisq statistic for each SNP as following:

Chisq EIGENSTRAT

1.2298 1.2695

1.2298 1.2695

1.6492 1.6652

1.2298 1.2695

1.0893 1.1060

0.9506 0.9554

0.9506 0.9554

2.9808 2.9909

2.9723 3.0327

1.8844 1.9356

... ....

How can I calculate the new corrected p values from these output?

Thank you

eigenstrat population • 397 views
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