Simulation

Schematic overview of various simulation settings

R scripts

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
    )