Package index • mrpipeline

MR Analysis

Run Mendelian randomisation and inspect results.

run_mr(): Perform Mendelian randomisation analysis
print(<mr_result>): Print an mr_result object
summary(<mr_result>): Summarise an mr_result object
plot(<mr_result>): Plot an mr_result object

Colocalization

Run colocalization analysis and inspect results.

run_coloc(): Perform colocalization analysis
print(<coloc_result>): Print a coloc_result object
summary(<coloc_result>): Summarise a coloc_result object
plot(<coloc_result>): Plot a coloc_result object

Data Formatting

Format proteomics GWAS data for use with mrpipeline.

format_pqtl_decode(): Formats deCODE genetics proteomic data for Mendelian Randomization analysis
format_pqtl_ukbppp(): Formats pQTL data from UKB-PPP for MR analysis.
format_single_cell_onek1k(): Format single-cell RNA eQTL data for analysis
decode_pqtl_file_name(): DECODE_PQTL_FILE_NAME
ukbppp_pqtl_file_name(): UKBPPP_PQTL_FILE_NAME

Utilities

Helper functions for analysis workflows.

get_gene_coords(): Look up gene coordinates from Ensembl via biomaRt