## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval = FALSE------------------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("GenomicSuperSignature") ## ----results="hide", message=FALSE, warning=FALSE----------------------------- library(GenomicSuperSignature) ## ----load_model--------------------------------------------------------------- RAVmodel <- getModel("C2", load=TRUE) ## ----------------------------------------------------------------------------- RAVmodel version(RAVmodel) geneSets(RAVmodel) ## ----------------------------------------------------------------------------- class(RAVindex(RAVmodel)) dim(RAVindex(RAVmodel)) RAVindex(RAVmodel)[1:4, 1:4] ## ----------------------------------------------------------------------------- names(metadata(RAVmodel)) ## ----------------------------------------------------------------------------- head(metadata(RAVmodel)$cluster) head(metadata(RAVmodel)$size) metadata(RAVmodel)$k metadata(RAVmodel)$n geneSets(RAVmodel) head(metadata(RAVmodel)$MeSH_freq) updateNote(RAVmodel) metadata(RAVmodel)$version ## ----------------------------------------------------------------------------- length(studies(RAVmodel)) studies(RAVmodel)[1:3] ## ----------------------------------------------------------------------------- PCinRAV(RAVmodel, 2) ## ----------------------------------------------------------------------------- x <- silhouetteWidth(RAVmodel) head(x) # average silhouette width of the first 6 RAVs ## ----------------------------------------------------------------------------- class(gsea(RAVmodel)) class(gsea(RAVmodel)[[1]]) length(gsea(RAVmodel)) gsea(RAVmodel)[1] ## ----------------------------------------------------------------------------- length(mesh(RAVmodel)) mesh(RAVmodel)[1] ## ----------------------------------------------------------------------------- length(PCAsummary(RAVmodel)) PCAsummary(RAVmodel)[1] ## ----------------------------------------------------------------------------- sessionInfo()