metaxcanr

An R alternative to MetaXcan

more details on method

for more details on metaxcan method refer to Metaxcan/Predixcan authors' repo (https://github.com/hakyimlab/MetaXcan)

installation

library(devtools)
install_github("drveera/metaxcanr")

usage

library(metaxcanr)

results <- metaxcan(gwas.file = <gwas.filename>, db.file = <dbfile.name>, snpcov.file = <snpcov.filename>)

examples

download sample files

wget https://github.com/drveera/metaxcanexample/raw/master/sample.db
wget https://raw.githubusercontent.com/drveera/metaxcanexample/master/sample.gwas.summary
wget https://github.com/drveera/metaxcanexample/raw/master/sample.snpcov

open R and run the following commands

library(metaxcanr)
results <- metaxcan(gwas.file="sample.gwas.summary", db.file = "sample.db", snpcov.file="sample.snpcov")

Format of GWAS data

The gwas data should have columns: SNP, A1, A2, BETA, SE

If OR, change that to BETA by taking log(OR)

Its very important the above columns should be there in the gwas file

For Citation

Barbeira, A. N. et al. Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. bioRxiv 045260 (2017). doi:10.1101/045260

(link: https://www.biorxiv.org/content/early/2017/10/03/045260)