## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, cache=TRUE) ## ----load_pkgs, message=FALSE------------------------------------------------- library(consensusOV) library(Biobase) library(genefu) ## ----load_data, message=FALSE------------------------------------------------- data(GSE14764.eset) dim(GSE14764.eset) GSE14764.expression.matrix <- exprs(GSE14764.eset) GSE14764.expression.matrix[1:5,1:5] GSE14764.entrez.ids <- fData(GSE14764.eset)$EntrezGene.ID head(GSE14764.entrez.ids) ## ----subtyping---------------------------------------------------------------- bentink.subtypes <- get.subtypes(GSE14764.eset, method = "Bentink") bentink.subtypes$Bentink.subtypes konecny.subtypes <- get.subtypes(GSE14764.eset, method = "Konecny") konecny.subtypes$Konecny.subtypes helland.subtypes <- get.subtypes(GSE14764.eset, method = "Helland") helland.subtypes$Helland.subtypes ## ----subtyping2, results="hide"----------------------------------------------- verhaak.subtypes <- get.subtypes(GSE14764.eset, method = "Verhaak") ## ----subtyping3--------------------------------------------------------------- verhaak.subtypes$Verhaak.subtypes consensus.subtypes <- get.subtypes(GSE14764.eset, method = "consensusOV") consensus.subtypes$consensusOV.subtypes ## ----alternative_subtyping---------------------------------------------------- ## Alternatively, e.g. bentink.subtypes <- get.subtypes(GSE14764.expression.matrix, GSE14764.entrez.ids, method = "Bentink") ## ----subtyping_ex_2----------------------------------------------------------- bentink.subtypes <- get.bentink.subtypes(GSE14764.expression.matrix, GSE14764.entrez.ids) ## ----verhaak_helland, fig.height = 8, fig.width = 8--------------------------- vest <- verhaak.subtypes$gsva.out vest <- vest[,c("IMR", "DIF", "PRO", "MES")] hest <- helland.subtypes$subtype.scores hest <- hest[, c("C2", "C4", "C5", "C1")] dat <- data.frame( as.vector(vest), rep(colnames(vest), each=nrow(vest)), as.vector(hest), rep(colnames(hest), each=nrow(hest))) colnames(dat) <- c("Verhaak", "vsc", "Helland", "hsc") ## plot library(ggplot2) ggplot(dat, aes(Verhaak, Helland)) + geom_point() + facet_wrap(vsc~hsc, nrow = 2, ncol = 2) ## ----konecny_helland, fig.height = 8, fig.width = 8--------------------------- kost <- konecny.subtypes$spearman.cc.vals hest <- helland.subtypes$subtype.scores hest <- hest[, c("C2", "C4", "C5", "C1")] dat <- data.frame( as.vector(kost), rep(colnames(kost), each=nrow(kost)), as.vector(hest), rep(colnames(hest), each=nrow(hest))) colnames(dat) <- c("Konecny", "ksc", "Helland", "hsc") ## plot ggplot(dat, aes(Konecny, Helland)) + geom_point() + facet_wrap(ksc~hsc, nrow = 2, ncol = 2)