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cuelee / pleio

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Standardization of effect sizes #2

Open sevi2018 opened 3 years ago

sevi2018 commented 3 years ago

Hi, I am testing pleio using a 90& of binary traits and remaining quantitative traits. I am wondering if the standardization of the effect sizes is implemented in pleio or if I have to do that by myself.

Another question is in the meta-analysis, does pleio have a function to compute a beta and se?

Thank you

cuelee commented 3 years ago

Hi, PLEIO uses standardized beta_estimates and se_estimates as inputs, which requires preprocessing of the raw summary statistics(You can do this manually). To simplify this preprocessing, we implemented an automation code in PLEIO package (which is the Python code: pleio/ldsc_preprocess). This automation code generates three input files required for PLEIO analysis. More information can be found at: LINK. Note that LDSC package must be installed to estimate the genetic covariance matrix and the environmental correlation matrix across multiple traits.

The current version of "PLEIO" does not provide a function to calculate "beta_estimate" and "se_estimate". We will update this feature later.

If you choose to use the automation code(ldsc_preprocess), please update PLEIO to the latest version using the following command from the path where PLEIO is installed:

git pull

Thank you