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Run multi-trait colocalization using HyPrColoc

Source: R/hyprcoloc_df.R
hyprcoloc_df.Rd

This function is a convenience wrapper around hyprcoloc::hyprcoloc() that takes a dataframe as input, and performs mutli-trait colocalization. Details of the HyPrColoc method are described in Foley et al. (Nature Communications 2021; https://doi.org/10.1038/s41467-020-20885-8).

Usage

hyprcoloc_df(
  df,
  trait_col = trait,
  snp_col = rsid,
  beta_col = beta,
  se_col = se,
  type_col = type,
  ...
)

Arguments

df

Dataframe containing summary statistics at a single locus, in a "long" format, with one row per variant per trait.

trait_col

Column containing trait names

snp_col

Column containing variant names (eg. rsid, marker_name), which should be consistent across studies

beta_col

Column containing effect estimates from GWAS

se_col

Column containing standard errors of the effect estimates

type_col

Column containing the "type" of trait - this column should contain 1 for binary traits, and 0 for all others

...

Arguments passed to hyprcoloc::hyprcoloc()

Value

A list containing a data.frame of HyPrColoc results: each row is a cluster of colocalized traits or is coded NA (if no colocalization is identified)

See also

Other colocalization: coloc_run()

Examples

if (FALSE) {
hyprcoloc_df(gwas_results_df)
}