## ----fig.height = 6, eval = FALSE--------------------------------------------- # TCGA.pipe("LUSC", # wd = "./ELMER.example", # cores = parallel::detectCores()/2, # mode = "unsupervised" # permu.size = 300, # Pe = 0.01, # analysis = c("distal.probes","diffMeth","pair","motif","TF.search"), # diff.dir = "hypo", # rm.chr = paste0("chr",c("X","Y"))) ## ----fig.height = 6, eval = FALSE--------------------------------------------- # TCGA.pipe("LUSC", # wd = "./ELMER.example", # cores = parallel::detectCores()/2, # mode = "supervised" # genes = "TP53", # group.col = "TP53", # group1 = "Mutant", # group2 = "WT", # permu.size = 300, # Pe = 0.01, # analysis = c("download","diffMeth","pair","motif","TF.search"), # diff.dir = "hypo", # rm.chr = paste0("chr",c("X","Y"))) ## ----sessioninfo, eval=TRUE--------------------------------------------------- sessionInfo()