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Formats deCODE genetics proteomic data for Mendelian Randomization analysis

format_pqtl_decode.Rd

This function filters deCODE genetics GWAS by the deCODE included variants file, processes the data to clean the column headings and uses TwoSampleMR::format_data() to prepare the exposure dataset before run_mr()

Usage

format_pqtl_decode(
  decode_proteomic_gwas_file_path,
  decode_included_variants_file_path,
  pqtl_assay,
  x_y_chr_file = NULL
)

Arguments

decode_proteomic_gwas_file_path

Character vector of file path(s) to deCODE GWAS data, or a single pre-loaded data.frame. If multiple paths are provided, data will be combined.

decode_included_variants_file_path

Character vector of file path(s) to the deCODE included variants data, or a single pre-loaded data.frame. If multiple paths are provided, data will be combined.

pqtl_assay

String, name of the deCODE genetics protein assayed

x_y_chr_file

String, optional file path to a file containing rsids for X and Y chromosomes. This file should be tab-separated with columns: Chromosome, Position, RSID.

Value

A list with two elements:

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

Examples

if (FALSE) { # \dontrun{
result <- format_pqtl_decode(
  decode_proteomic_gwas_file_path = "path/to/decode_gwas.txt.gz",
  decode_included_variants_file_path = "path/to/included_variants.txt.gz",
  pqtl_assay = "CD40"
)
head(result$exposure)
} # }