Case control status permutation in GWAS
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4.3 years ago
mel22 ▴ 100

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

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

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

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