cophe_plot: cophe_plots showing the Ha and Hc of all traits and labelled...

In ichcha-m/cophescan: Adaptation of the Coloc Method for PheWAS

cophe_plots showing the Ha and Hc of all traits and labelled above the specified threshold

Description

cophe_plots showing the Ha and Hc of all traits and labelled above the specified threshold

Usage

cophe_plot(
  multi.dat,
  querysnpid,
  query_trait_names,
  thresh_Hc = 0.5,
  thresh_Ha = 0.5,
  beta_p = NULL,
  traits.dat = NULL,
  group_pheno = NULL
)

Arguments

multi.dat	multi trait cophescan results returned from cophe.multitrait or multitrait.simplify
querysnpid	query variant (only a single variant for PheWAS plots)
query_trait_names	list of phenotype names
thresh_Hc	Hc threshold to be displayed
thresh_Ha	Ha threshold to be displayed
beta_p	data.frame (from the get.beta function) with four columns : 1. "beta_plot": indicating beta direction (p or n) 2. "beta_plot": -log10(pval) of the queried variant 3. "querysnp" 4. "querytrait".
traits.dat	list of multi-trait coloc structured datasets
group_pheno	Vector with additional grouping of phenotypes

Value

cophescan plots of Ha and Hc

See Also

cophe.single, cophe.susie, cophe.multitrait, , multitrait.simplify

ichcha-m/cophescan documentation built on June 16, 2024, 1:39 a.m.