cophescan (version 1.4.2)

cophe.susie: run cophe.susie using susie to detect separate signals

Description

Check if a variant causally associated in one trait might be causal in another trait

Usage

cophe.susie(
  dataset,
  querysnpid,
  querytrait,
  pa = 3.82e-05,
  pc = 0.00182,
  p1 = NULL,
  p2 = NULL,
  p12 = NULL,
  susie.args = list()
)

Value

a list, containing elements

• summary a data.table of posterior probabilities of each global hypothesis, one row per pairwise comparison of signals from the two traits

• results a data.table of detailed results giving the posterior probability for each snp to be jointly causal for both traits assuming Hc is true. Please ignore this column if the corresponding posterior support for H4 is not high.

• priors a vector of the priors used for the analysis

Arguments

dataset

either a list with specifically named elements defining the dataset to be analysed. (see check_dataset)

querysnpid

Id of the query variant

querytrait

Query trait name

pa

prior probability that a non-query variant is causally associated with the query trait (cophescan prior), default 3.82e-5

pc

prior probability that the query variant is causally associated with the query trait (cophescan prior), default 1.82e-3

p1

prior probability a SNP is associated with trait 1, (coloc prior), pc derived by using \(pc = p12/p1+p12\); use p1, p2, p12 only when pa and pc are unavailable (See vignettes)

p2

prior probability a SNP is associated with trait 2, (coloc prior), pa derived by using \(pa = p2\)

p12

prior probability a SNP is associated with both traits, (coloc prior), pc derived by using \(pc = p12/p1+p12\)

susie.args

a named list of additional arguments to be passed to runsusie

Author

Ichcha Manipur

Examples

library(cophescan)
data(cophe_multi_trait_data)
query_trait_1 <- cophe_multi_trait_data$summ_stat[['Trait_1']]
querysnpid <- cophe_multi_trait_data$querysnpid
query_trait_1$LD <- cophe_multi_trait_data$LD
res.susie <- cophe.susie(query_trait_1, querysnpid = querysnpid, querytrait='Trait_1')
summary(res.susie)