## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("GOpro", dependencies = TRUE) ## ----eval=TRUE, results='hide', warning=FALSE, message=FALSE------------------ library(GOpro) ## ----cache=TRUE, message=FALSE, results='markup'------------------------------ exrtcga ## ----results='hold', message=FALSE, cache=TRUE-------------------------------- findGO(exrtcga) ## ----results='hold', message=FALSE, cache=TRUE-------------------------------- findGO(exrtcga, extend = TRUE) ## ----results='markup', message=FALSE, cache=TRUE, fig.keep='all', fig.show='hold', dev='png'---- findGO(exrtcga, topGO = 2, grouped = 'clustering') ## ----results='markup', message=FALSE, cache=TRUE, fig.keep='all', fig.show='hold', dev='png'---- findGO(exrtcga, topGO = 2, grouped = 'clustering', over.rep = TRUE)