cophe.susie.lbf: cophe.susie.lbf

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

cophe.susie.lbf

Description

Calculate log bayes factors for each hypothesis (SuSIE - multiple causal variant assumption)

Usage

cophe.susie.lbf(
  dataset,
  querysnpid,
  querytrait,
  switch = TRUE,
  susie.args = list(),
  MAF = NULL
)

Arguments

dataset	a list with specifically named elements defining the query trait dataset to be analysed.
querysnpid	Id of the query variant, (id in dataset$snp)
querytrait	Query trait name
switch	Set switch=TRUE to obtain single BF when credible sets not found with SuSIE
susie.args	a named list of additional arguments to be passed to runsusie
MAF	Minor allele frequency vector

Value

data frame with log bayes factors for Hn and Ha hypotheses

Author(s)

Ichcha Manipur

See Also

cophe.susie

Examples

library(cophescan)
data(cophe_multi_trait_data)
query_trait_1 <- cophe_multi_trait_data$summ_stat[['Trait_1']]
query_trait_1$LD <- cophe_multi_trait_data$LD
querysnpid <- cophe_multi_trait_data$querysnpid
res.susie.lbf <- cophe.susie.lbf(query_trait_1, querysnpid = querysnpid,
                                  querytrait='Trait_1', switch=T)
res.susie.lbf

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