devtools::install_github("ShouyeLiu/SBayesOmics")

rm(list = ls())
library(SBayesOmics)
datPathInPack <- system.file("extdata/pseudo1kgchr22", package = "SBayesOmics")
trainBfilePrefix <- "psuedo-1kg-chr22-causal-model-ind-10k-snp-11555"

paramSuffix = "1kg-cis-50k-"

trainBfile <- paste0(datPathInPack,"/",trainBfilePrefix)

snp2ldFile <-    paste0(paramSuffix,"sub-all-block-chr22-ld-2-snp-map.rds")
WithoutLDAllSNP2GeneFile <- paste0(paramSuffix,"sub-all-block-","chr22-snp-2-gene-map.rds")

mapSnpGeneAcrossChrFile <- paste0(datPathInPack,"/",WithoutLDAllSNP2GeneFile)
mapLd2SnpFile <- paste0(datPathInPack,"/",snp2ldFile)

  sim <-  simGWASMainOverlap(isIndLevelBool = TRUE,
                               seed = 1,
                               trainBfile,
                               mapSnpGeneAcrossChrFile,
                               mapLd2SnpFile,
                               simModel = "b",  ## a: causal model only; b: pleitropic model only; c: intergenic model only
                               geneOverlap = "c", ## random overlap
                               traitType = "a", ## continuous traits
                               indNum = 2000, ## gwas number
                               NumCGCau = 10, ## number of causal genes
                               NumCVPerGCau = 10,   ### number of causal variants per gene
                               NumCGPle = 10,   ## number of causal pleiotropic genes;
                               NumCVPerGPle = 10, ## number of causal variants per pleiotropic gene
                               NumCGNull  = 10, ### number of null gene
                               NumCVPerGNull = 10, ### number of causal variants per null gene
                               NumCVIG = 10,  ## number of causal variants in intergenic region
                               realGeno = TRUE,
                               ldwBool = TRUE,
                               cisOnly = TRUE,
                               h2cis = 0.5, ## cis-heritability
                               h2snp = 0.1, ## total snp heritability
                               h2med = 0.05, ## mediated heritability
                               outPath = "", 
                               smrPath = "" ,
                               totalOverlapBool = FALSE,
                               smrIndGenePath = "",
                               smrIndFileSuffix = "mac",
                               cauPleWithinGene = FALSE
        )