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Overview

If you are new to PLEIO, you can proceed with the analysis by following the instructions provided below.

Executable files

1. pleio.py pleio.py is a python code that can analyze multiple GWAS summary statistics to test per-SNP associations. This python executable requires three inputs:

• summary statistics on a standardized scale
• Genetic covariance matrix between traits
• Environmental(Non-genetic) correlation matrix between traits

If you are unsure whether your summary statistics are standardized, please refer to ldsc_preprocess.py for standardization of effect sizes.)

2. ldsc_preprocess.py ldsc_preprocess.py is a python code that can convert a set of raw GWAS summary statistics into pleio.py's inputs. ldsc_preprocess.py uses other 3rd party software ldsc to estimate genetic covariance and environmental correlation matrices. This python executable requires three inputs:

• A text file containing traits' information, which contains
  • path to summary statistics
  • trait sample & population prevalence
  • the type of each trait (binary or quantitative)
• LD scores generated by the reference panel