## ----reqs, echo=FALSE, message=FALSE------------------------------------------ suppressMessages(library(tmle)) suppressMessages(library(minfi)) suppressMessages(library(SummarizedExperiment)) ## ----prelims------------------------------------------------------------------ library(methyvim) library(methyvimData) ## ----get-data----------------------------------------------------------------- set.seed(479253) data(grsExample) grsExample var_int <- as.numeric(colData(grsExample)[, 1]) table(var_int) ## ----make-methytmle----------------------------------------------------------- mtmle <- .methytmle(grsExample) ## ----methyvim-ate-sl---------------------------------------------------------- suppressMessages( methyvim_ate_sl <- methyvim(data_grs = grsExample, sites_comp = 25, var_int = var_int, vim = "ate", type = "Mval", filter = "limma", filter_cutoff = 0.10, parallel = FALSE, tmle_type = "sl" ) ) ## ----methyvim-ate-sl-print---------------------------------------------------- vim(methyvim_ate_sl) ## ----methyvim-ate-glm--------------------------------------------------------- suppressMessages( methyvim_ate_glm <- methyvim(data_grs = grsExample, sites_comp = 25, var_int = var_int, vim = "ate", type = "Mval", filter = "limma", filter_cutoff = 0.10, parallel = FALSE, tmle_type = "glm" ) ) ## ----methyvim-ate-glm-print--------------------------------------------------- vim(methyvim_ate_glm) ## ----methyvim-rr-sl----------------------------------------------------------- methyvim_rr_sl <- methyvim(data_grs = grsExample, sites_comp = 25, var_int = var_int, vim = "rr", type = "Mval", filter = "limma", filter_cutoff = 0.10, parallel = FALSE, tmle_type = "sl" ) ## ----methyvim-rr-sl-print----------------------------------------------------- vim(methyvim_rr_sl) ## ----methyvim-rr-glm---------------------------------------------------------- methyvim_rr_glm <- methyvim(data_grs = grsExample, sites_comp = 25, var_int = var_int, vim = "rr", type = "Mval", filter = "limma", filter_cutoff = 0.10, parallel = FALSE, tmle_type = "glm" ) ## ----methyvim-rr-glm-print---------------------------------------------------- vim(methyvim_rr_glm) ## ----setup-minfidata---------------------------------------------------------- suppressMessages(library(minfiData)) data(MsetEx) mset <- mapToGenome(MsetEx) grs <- ratioConvert(mset) grs ## ---- minfidata-maketx-------------------------------------------------------- var_int <- (as.numeric(as.factor(colData(grs)$status)) - 1) table(var_int) ## ---- minfidata-methyvim, eval=FALSE------------------------------------------ # suppressMessages( # methyvim_cancer_ate <- methyvim(data_grs = grs, var_int = var_int, # vim = "ate", type = "Beta", filter = "limma", # filter_cutoff = 0.30, obs_per_covar = 2, # parallel = FALSE, sites_comp = 50, # tmle_args = list(cv_folds = 2), # tmle_type = "sl" # ) # ) ## ----vim-cancer-ate, eval=FALSE----------------------------------------------- # methyvim_cancer_ate ## ----fdr-msa, eval=FALSE------------------------------------------------------ # fdr_p <- fdr_msa(pvals = vim(methyvim_cancer_ate)$pval, # total_obs = nrow(methyvim_cancer_ate)) ## ----methyvim-pvals-both, eval=FALSE------------------------------------------ # plot(methyvim_cancer_ate) ## ----methyvim-volcano, eval=FALSE--------------------------------------------- # methyvolc(methyvim_cancer_ate) ## ----methyvim-heatmap, eval=FALSE--------------------------------------------- # methyheat(methyvim_cancer_ate) ## ----session-info, echo=FALSE------------------------------------------------- sessionInfo()