## ----setup_data, message=FALSE--------------------------------------------- library(adaptest) data(simpleArray) set.seed(1234) Y <- simulated_array A <- simulated_treatment ## ----adaptest_eval, message=FALSE------------------------------------------ adaptest_out <- adaptest(Y = Y, A = A, W = NULL, n_top = 35, n_fold = 5, learning_library = c("SL.glm", "SL.mean"), parameter_wrapper = adaptest::rank_DE, absolute = FALSE, negative = FALSE) ## ----get_comp_small-------------------------------------------------------- get_composition(object = adaptest_out, type = "small") ## ----get_comp_big---------------------------------------------------------- get_composition(object = adaptest_out, type = "big") ## ----plot------------------------------------------------------------------ plot(adaptest_out) ## ----sum_exp, message=FALSE------------------------------------------------ library(SummarizedExperiment) library(airway) data(airway) ## ----augment_se------------------------------------------------------------ genes_sub <- order(sample(seq_len(1000))) air_reduced <- airway[genes_sub, ] ## ----augment_airway-------------------------------------------------------- simple_air <- cbind(air_reduced, air_reduced) ## ----make_tx_var----------------------------------------------------------- # use a binary treatment variable (must be 0/1 only) dex_var = as.numeric(as.matrix(colData(simple_air))[, 3] - 1) ## ----bioadaptest----------------------------------------------------------- airway_out <- bioadaptest(data_in = simple_air, var_int = dex_var, cntrl_set = NULL, n_top = 5, n_fold = 2, parameter_wrapper = rank_DE) ## ----session_info, echo=FALSE---------------------------------------------- sessionInfo()