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

Source: R/copheplots.R

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

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