## ----eval=FALSE--------------------------------------------------------------- # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("INTACT") ## ----------------------------------------------------------------------------- library(INTACT) data(simdat) rst <- INTACT::intact(GLCP_vec=simdat$GLCP, z_vec=simdat$TWAS_z) ## ----------------------------------------------------------------------------- rst1 <- INTACT::intact(GLCP_vec=simdat$GLCP, prior_fun=INTACT::expit, z_vec = simdat$TWAS_z, t = 0.02,D = 0.09) rst2 <- INTACT::intact(GLCP_vec=simdat$GLCP, prior_fun=INTACT::step, z_vec = simdat$TWAS_z, t = 0.49) rst3 <- INTACT::intact(GLCP_vec=simdat$GLCP, prior_fun=INTACT::hybrid, z_vec = simdat$TWAS_z, t = 0.49,D = 0.05) ## ----------------------------------------------------------------------------- fdr_example <- fdr_rst(rst1, alpha = 0.05) head(fdr_example) ## ----------------------------------------------------------------------------- data(gene_set_list) INTACT::intactGSE(gene_data = simdat,gene_sets = gene_set_list) ## ----------------------------------------------------------------------------- INTACT::intactGSE(gene_data = simdat,prior_fun = INTACT::step, t = 0.45,gene_sets = gene_set_list) INTACT::intactGSE(gene_data = simdat,prior_fun = INTACT::expit, t = 0.08,D = 0.08, gene_sets = gene_set_list) INTACT::intactGSE(gene_data = simdat,prior_fun = INTACT::hybrid, t = 0.08,D = 0.08, gene_sets = gene_set_list) ## ----------------------------------------------------------------------------- sessionInfo()