README.md

Post-GWAS analysis and Mendelian Randomization

During the study based on Mendelian Randomization, several functions were proposed to solve several common problems, including:

Special note

Recently, I noticed that some uploaders in Bilibili seem to sell my codes. The original purpose of this project is to share my solutions to certain problems in Mendelian Randomization without charge. I urge those guys stop selling my codes, and I decide to not share my recent findings on MR. If you have any questions, leave me a message. Additionally, students from the Department of Neurology, Xiangya Hospital are not allowed to use my codes.

Preprocessing for exposure GWASs

• how to get rsID from chromosome and position: get_rsID_from_chr_pos
• how to find allele frequency, proxy of a given SNP: snp_add_eaf, snp_add_eaf_manual,find_proxy
• how to search pleiotropy for a given SNP: snp_phenoscanner

Exposure and outcome data harmonization

• how to harmonize if direct removal is not allowed and proxy is required: snp_replace_proxy, harmonise_data_modified

Main analysis for Mendelian Randomization

• mr_meta is helpful conduct meta-analysis to pool estimates from different cohorts
• mr_modified is alternative function to mr in TwoSampleMR package, since the mr-raps cannot not be conducted in the original function
• get_cohort_from_number transforms a number into a name of cohort
• get_method_from_abbr transforms an abbreviation version of MR method into a full name
• get_protein_from_uniprot transforms a UniProt ID to full name of protein, with UniProtRefPanel.xlsx as the reference panel

More functions are under developing...

• data visualization: volcano plot, forest plot...
• colocolization
• TWAS
• ...

Useful references

• MR dictionary
• Cohorts: FinnGen, UK Biobank
• Algorithm: MR-RAPS, MR-PRESSO, MR-Mix, IMRP, MR-GENIUS, MR-AID, MR-TRYX, NLMR, MVMR, BayesMR, CFMR, OMR, MR-JTI
• Packages: ieugwasr