## ----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()