Question: calculate f statistic for SNPs from GWAS
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gravatar for mk19726
7 months ago by
mk1972610
mk1972610 wrote:

Hi,

I have two different types of list of SNPs for MR analysis. One list is just the significant SNPs from a published GWAS (not the whole summary data). Other lists of SNPs have the whole summary data

In R I would like to calculate the overall F statistic to assess instrument strength.

I saw a paper where they wrote this, "we estimated the r2 of each genetic instrument and summed them up to compute the overall r2 and F statistics using the sample size "

I would love to do this with my data too!

Can anyone explain how to do this in R?

I have rsid, beta, se, pval, N

Incase this effects things, one of my SNP lists for which I have summary data is binary, all others continuous

Thank you for your help!!!

snp R • 395 views
ADD COMMENTlink modified 4 months ago by panmy20150 • written 7 months ago by mk1972610

Yes,I have the same question as you, have you got any answers?

ADD REPLYlink written 4 months ago by panmy20150
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