Meta-analysis in PLINK - What to use in order to do a forest plot
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Entering edit mode
5.6 years ago

I am doing a meta-analysis using PLINK.

I have the *.assoc files for each study and I have used the --meta-analysis + qt study weighted-z options.

I have the following questions in order to do a forest plot:

1) I need the beta and SE of the meta-analysis. PLINK provides a BETA (fixed model), but not the SE. How do I compute it? I would thought I would get one, but otherwise should I use:

SE = SQRT ( 1/ SUM weights)

Where the weights = the inverse variance

2) I also need the beta and corresponding SE of each study for the forest plot. However, when I check the indvidual *.assoc files and the last columns on the *.meta files, the betas are different. Why?

meta-analysis plink beta • 3.5k views
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Entering edit mode

Hi,

Don't know if it's the right place but how did you convert the plink output (plink.meta) file into a format readable by R. Thought I'd ask here as you seem to have done a meta-analysis.

Thanks

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Entering edit mode

You can import it directly in R as any txt file

0
Entering edit mode

Hi,

Don't know if it's the right place but how did you convert the plink output (plink.meta) file into a format readable by R. Thought I'd ask here as you seem to have done a meta-analysis.

Thanks

0
Entering edit mode
5.6 years ago

Found an answer on the PLINK forum for my second question. The results of the beta are on the exp scale, but this was changed in a later update!

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Entering edit mode
5.2 years ago

Add " --ci 0.95 " command, then it will output SE and CI.