cophe.susie.lbf

Source: R/multivarsusie.R

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

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

See also

cophe.susie

Author

Ichcha Manipur

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)
#> running max iterations: 100
#> 	converged: TRUE
res.susie.lbf
#>      lBF.Ha   lBF.Hc nsnps       querysnp querytrait           hit1
#> 1: 15.31003 11.95277  1000 chr19-11182353    Trait_1 chr19-11182353
#>              hit2  typeBF idx1 idx2
#> 1: chr19-11182144 susieBF    1    1