Case control status permutation in GWAS

Hi, I performed 10E6 case/control status permutations for GWAS data. NOw, for each SNP I have 10e6 p_value, I wonder what is the best graphic presentation to use for permutation results ? Any example is welcome !!

Thank you !

snp r

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written 6.6 years ago by mel22

Aren't you supposed to calculate p-values from the permuted data? And then just use Manhattan plot?

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written 6.6 years ago by German.M.Demidov

Hi German.M.Demidov , thanks for your reply , How can I calculate the p_value from permuted data ?

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written 6.6 years ago by mel22

By definition - number of times your permuted statistic is bigger/smaller than the observed one

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written 6.6 years ago by German.M.Demidov

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