cophescan (version 1.4.2)

cophe.susie.lbf: 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
)

Value

data frame with log bayes factors for Hn and Ha hypotheses

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

Author

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