Scripts for analysis of GWAS results.
These scripts integrate several eQTL databases to look for genetic effects of SNPs identified by GWAS.
You can install the package by running the following command from the package's root directory:
pip install -e .The package can then be imported as
import ImmuneGWAS
After you have installed the package, you will need to update the configuration file. Copy the
ImmuneGWAS/config.dist.py file and rename it to ImmuneGWAS/config.py. Change the default paths in the file to
the correct paths to cbio3 and the desired output folder.
Start your analysis by creating a new Variant object for the SNP you want to analyze. You can either provide the
complete information about the SNP like so: Variant(rsid, chromosome, position, effect allele, other allele) or just
the rsid: Variant.from_rsid(rsid). The latter will only work if the variant is present in our GWAS summary statistics.
Once you have created the Variant object, you can use it to query the eQTL databases. For example, to get all the cis-eQTLs from eQTLGen for the variant, you can run:
eqtlgen_cis_LDblock_query(Variant)
This will update the contents of the .results attribute of the object with the results from the query. You can get
those results by running:
Variant.results.eqtlgen_cis()
The following databases are available, listed here under the names used in the scripts:
- Tokyo: a database of eQTLs from the ImmuneXUT project, from the University of Tokyo. Cell. 2021; 184(11): 3006-3021
- eQTL cat: a database of eQTLs from the eQTL Catalogue project, by EMBL-EBI.
- eQTLGen: a database of eQTLs by the eQTLGen Consortium. Both cis-eQTL and trans-eQTL datasets are available.