Post-GWAS analysis and Mendelian Randomization

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

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

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

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