cophe.multitrait {cophescan}

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

Author(s)

Ichcha Manipur