cophe.multitrait: Run cophescan on multiple traits at once
In ichcha-m/cophescan: Adaptation of the Coloc Method for PheWAS

cophe.multitrait

R Documentation

Run cophescan on multiple traits at once

Description

Run cophescan on multiple traits at once

Usage

cophe.multitrait(
  trait.dat,
  querysnpid,
  querytrait.names,
  LDmat = NULL,
  method = "single",
  simplify = FALSE,
  predict.hyp = TRUE,
  Hn.cutoff = 0.2,
  Hc.cutoff = 0.6,
  est.fdr.based.cutoff = FALSE,
  fdr = 0.05,
  ...
)

Arguments

`trait.dat`	Named(traits) list of coloc structured data for k traits (Total number of traits)
`querysnpid`	vector of query variant ids = length(trait.dat), if the same variant
`querytrait.names`	vector of names for the query traits, if the names of the multi.dat list contain the trait names please pass querytrait.names=names(multi.dat)
`LDmat`	LD matrix
`method`	either 'single' for `cophe.single` or 'susie' for `cophe.susie`
`simplify`	if TRUE removes intermediate results from output using 'multitrait.simplify'
`predict.hyp`	if TRUE predicts the hypothesis based on the provided thresholds for pp.Hc and pp.Hn (overrides simplify) using `cophe.hyp.predict`
`Hn.cutoff`	threshold for PP.Hc above which the associations are called Hc
`Hc.cutoff`	threshold for PP.Hc above which the associations are called Hn
`est.fdr.based.cutoff`	if True calculates the Hc.cutoff using 1-mean(PP.Hc)\|PP.Hc > cutoff
`fdr`	fdr threshold to estimate Hc.cutoff
`...`	additional arguments of priors for `cophe.susie` or `cophe.single`

Value

if simplify is False returns multi-trait list of lists, each with:

a summary data.frame of the cophescan results
priors used
querysnp
querytrait

if simplify is TRUE only returns dataframe with posterior probabilties of Hn, Hc and Ha with no intermediate results if predict.hyp is TRUE returns a dataframe with output of simplify and the predicted hypotheses for all associations