cophe.susie.lbf | R Documentation |
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
)
dataset |
a list with specifically named elements defining the query trait dataset to be analysed. |
querysnpid |
Id of the query variant, (id in dataset$snp) |
querytrait |
Query trait name |
switch |
Set switch=TRUE to obtain single BF when credible sets not found with SuSIE |
susie.args |
a named list of additional arguments to be passed to runsusie |
MAF |
Minor allele frequency vector |
data frame with log bayes factors for Hn and Ha hypotheses
Ichcha Manipur
cophe.susie
library(cophescan)
data(cophe_multi_trait_data)
query_trait_1 <- cophe_multi_trait_data$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
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