## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup, message = FALSE, results="hide", warning=FALSE, eval=FALSE-------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("MOMA") ## ----load--------------------------------------------------------------------- library(MOMA) ## ----explore data, message = FALSE-------------------------------------------- example.gbm.mae MultiAssayExperiment::assays(example.gbm.mae)$viper[1:3, 1:3] ## ----pathways----------------------------------------------------------------- names(gbm.pathways) gbm.pathways$cindy[1:3] ## ----moma object-------------------------------------------------------------- momaObj <- MomaConstructor(example.gbm.mae, gbm.pathways) ## ----interactions, results = "hide", message = FALSE-------------------------- momaObj$runDIGGIT() momaObj$makeInteractions() momaObj$Rank() ## ----clustering--------------------------------------------------------------- momaObj$Cluster() # Explore the reliability scores momaObj$clustering.results$all.cluster.reliability # Save in the 3 cluster solution momaObj$sample.clustering <- momaObj$clustering.results$`3clusters`$clustering ## ----saturation, message=FALSE, results="hide"-------------------------------- momaObj$saturationCalculation() ## ----checkpoints-------------------------------------------------------------- cluster1.checkpoint <- momaObj$checkpoints[[1]] print (cluster1.checkpoint[1:5]) ## ----make plots, warning=FALSE, include=FALSE--------------------------------- plots <- makeSaturationPlots(momaObj) ## ----visualize plots---------------------------------------------------------- library(ggplot2) library(grid) grid.draw(plots$oncoprint.plots[[3]]) plots$curve.plots[[3]] + ggtitle("Genomic Saturation Curve for GBM Subtype 3") ## ----saving data, eval=FALSE-------------------------------------------------- # momaObj$saveData(output.folder = "outputs", "hypotheses", "checkpoints") ## ----sessionInfo-------------------------------------------------------------- sessionInfo()