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Formats pQTL data from UKB-PPP for MR analysis.

format_pqtl_ukbppp.Rd

This function processes pQTL summary statistics from UKB-PPP, matches them with rsID information, handles non-Mendelian chromosomes, standardizes column names, and formats the data for use with the TwoSampleMR package.

Usage

format_pqtl_ukbppp(ukbppp, ukbppp_rsid, pqtl_assay, x_y_chr_file = NULL)

Arguments

ukbppp

Dataframe, file path to the file containing the ukbppp GWAS data

ukbppp_rsid

Dataframe, file path to the file containing the ukbppp GWAS data rsids

pqtl_assay

String, of the ukbppp protein assay

x_y_chr_file

Data frame or string file path containing rsIDs for X and Y chromosomes, or NULL. When a data frame is supplied, it is used directly (skipping fread()). When a string path is supplied, the file is read via data.table::fread().

Value

A list with two elements:

  • exposure: Formatted exposure data frame (output of TwoSampleMR::format_data).

Examples

# See the test script for example usage.