## ----"installation", eval=FALSE----------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("dorothea") ## ----"load packages", message = FALSE----------------------------------------- ## We load the required packages library(dorothea) library(bcellViper) library(dplyr) library(viper) ## ----"load data"-------------------------------------------------------------- # accessing expression data from bcellViper data(bcellViper, package = "bcellViper") # acessing (human) dorothea regulons # for mouse regulons: data(dorothea_mm, package = "dorothea") data(dorothea_hs, package = "dorothea") ## ----"run viper", message=FALSE----------------------------------------------- regulons = dorothea_hs %>% filter(confidence %in% c("A", "B")) tf_activities <- run_viper(dset, regulons, options = list(method = "scale", minsize = 4, eset.filter = FALSE, cores = 1, verbose = FALSE)) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()