# Define the list for the genotype data.
snp.list <- list()
snp.list$file <- system.file("sampleData", "geno_data.ldat.gz", package="CGEN")
snp.list$file.type <- 7
snp.list$delimiter <- "\t"
snp.list$in.miss <- " "
# Only process the first 5 SNPs in the file
snp.list$start.vec <- 1
snp.list$stop.vec <- 6
# Define pheno.list
pheno.list <- list()
pheno.list$file <- system.file("sampleData", "Xdata.txt", package="CGEN")
pheno.list$file.type <- 3
pheno.list$delimiter <- "\t"
pheno.list$id.var <- "id"
# Define the variables in the model
pheno.list$response.var <- "case.control"
pheno.list$strata.var <- "ethnic.group"
pheno.list$main.vars <- c("age.group", "oral.years", "n.children")
pheno.list$int.vars <- "n.children"
# Define the list of options
op <- list(out.file="out.txt")
# For this model, all variables are continuous
# temp <- GxE.scan(snp.list, pheno.list, op=op)
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