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MRCIEU / TwoSampleMR

R package for performing 2-sample MR using MR-Base database
https://mrcieu.github.io/TwoSampleMR
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New generate odds ratio function #65

Open jonnyrose opened 5 years ago

jonnyrose commented 5 years ago

Just to be sure, I understand this function is useful when outcome is a binary phenotype, where GWAS association method was logistics regression. What if the outcome is the ordered categorical type (e.g. frequency outcomes: never = 0, 1-2 times = 1, 3-6 times = 2, etc), but GWAS association method used was linear regression; the beta in the summary statistics would not be log odds of the outcome. Would it be valid to use generate_odds_ratio function in any case other than a binary phenotype from a GWAS estimated using logistic regression?

Thanks in advance for any help you can give me.

mightyphil2000 commented 5 years ago

Hi Jonnyrose

I recommend that the function is only used where the summary data has been derived from a logistic regression model of a binary phenotype.

bw

Philip

From: jonnyrose notifications@github.com Sent: 24 March 2019 17:28:01 To: MRCIEU/TwoSampleMR Cc: Subscribed Subject: [MRCIEU/TwoSampleMR] New generate odds ratio function (#65)

Just to be sure, I understand this function is useful when outcome is a binary phenotype, where GWAS association method was logistics regression. What if the outcome is the ordered categorical type (e.g. frequency outcomes: never = 0, 1-2 times = 1, 3-6 times = 2, etc), but GWAS association method used was linear regression; the beta in the summary statistics would not be log odds of the outcome. Would it be valid to use generate_odds_ratio function in any case other than a binary phenotype from a GWAS estimated using logistic regression?

Thanks in advance for any help you can give me.

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