## ----setup, include=FALSE, cache=FALSE, message = FALSE----------------------- library("knitr") ### Chunk options: see http://yihui.name/knitr/options/ ### ## Text results opts_chunk$set(echo = TRUE, warning = TRUE, message = TRUE, include = TRUE) ## Code decoration opts_chunk$set(tidy = FALSE, comment = NA, highlight = TRUE) ## ----knitcitation, include=FALSE---------------------------------------------- library(knitcitations) cleanbib() cite_options(citation_format = "pandoc") ## ----eval=FALSE--------------------------------------------------------------- # SE@annotation <- "rna" ## ----eval=FALSE--------------------------------------------------------------- # PharmacoSet(name, # molecularProfiles=list(), # cell=data.frame(), # drug=data.frame(), # sensitivityInfo=data.frame(), # sensitivityRaw=array(dim=c(0,0,0)), # sensitivityProfiles=matrix(), # curationDrug=data.frame(), # curationCell=data.frame(), # curationTissue=data.frame(), # datasetType=c("sensitivity", "perturbation", "both"), # verify = TRUE)