## ----setup, include=FALSE, cache=FALSE-------------------------------------------------- library(knitr) # set global chunk options opts_chunk$set(fig.path='figure/minimal-', fig.align='center', fig.show='hold') options(formatR.arrow=TRUE,width=90) ## ----checkinstall, eval=FALSE----------------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("consensus") ## ----loaddata, message=FALSE------------------------------------------------------------ library(consensus) data("TCGA") ## ----lookatdata------------------------------------------------------------------------- sapply(mget(c("U133A", "Huex", "Agilent", "RNASeq")), dim) rnames <- sapply(mget(c("U133A", "Huex", "Agilent", "RNASeq")), rownames) head(rnames) apply(rnames[,2:ncol(rnames)], 2, function (x) all(x==rnames[,1])) cnames <- sapply(mget(c("U133A", "Huex", "Agilent", "RNASeq")), colnames) head(cnames) apply(rnames[,2:ncol(rnames)], 2, function (x) all(x==rnames[,1])) rm(rnames, cnames) ## ----mm--------------------------------------------------------------------------------- tcga_mm <- MultiMeasure(names=c("U133A", "Huex", "Agilent", "RNA-Seq"), data=list(U133A, Huex, Agilent, RNASeq)) tcga_mm ## ----tp53------------------------------------------------------------------------------- plotOneFit(tcga_mm, "TP53", brewer.pal(n = 4, name = "Dark2")) ## ----fit-------------------------------------------------------------------------------- fit <- fitConsensus(tcga_mm) fit ## ----margave---------------------------------------------------------------------------- plotMarginals(fit, "average", brewer.pal(n = 4, name = "Dark2")) ## ----margsens--------------------------------------------------------------------------- plotMarginals(fit, "sensitivity", brewer.pal(n = 4, name = "Dark2")) ## ----margprec--------------------------------------------------------------------------- plotMarginals(fit, "precision", brewer.pal(n = 4, name = "Dark2")) ## ----pmdsens---------------------------------------------------------------------------- plotMostDiscordant(fit, "sensitivity", 15) ## ----my07b------------------------------------------------------------------------------ plotOneFit(tcga_mm, "MYO7B", brewer.pal(n = 4, name = "Dark2")) ## ----sessionInfo------------------------------------------------------------------------ sessionInfo()