Nothing
testpipeline <- function(){
data(TCGA)
# Test MultiMeasure()
#########################################
checkException(tcga_mm <- MultiMeasure(names=c("U133A", "Huex", "Agilent", "RNA-Seq"),
data=list(U133A[-1,], Huex, Agilent, RNASeq)))
badrowU133A <- badcolU133A <- U133A
rownames(badrowU133A) <- paste0("dummy", 1:nrow(badrowU133A))
colnames(badcolU133A) <- paste0("dummy", 1:ncol(badcolU133A))
checkException(tcga_mm <- MultiMeasure(names=c("U133A", "Huex", "Agilent", "RNA-Seq"),
data=list(badrowU133A, Huex, Agilent, RNASeq)))
checkException(tcga_mm <- MultiMeasure(names=c("U133A", "Huex", "Agilent", "RNA-Seq"),
data=list(badcolU133A, Huex, Agilent, RNASeq)))
checkException(tcga_mm <- MultiMeasure(names=c("U133A", "Huex", "Agilent", "RNA-Seq"),
data=list(U133A, Huex, Agilent)))
checkException(tcga_mm <- MultiMeasure(names=c("U133A", "Huex"),
data=list(U133A, Huex)))
###############################################################
tcga_mm <- MultiMeasure(names=c("U133A", "Huex", "Agilent", "RNA-Seq"),
data=list(U133A, Huex, Agilent, RNASeq))
#Test fitConsensus
##################################################################################
checkException(fitConsensus(1))
###################################################################################
fit <- fitConsensus(tcga_mm)
#Test plotOneFit()
#########################################################################
checkException(plotOneFit(1, "TP53", brewer.pal(n = 4, name = "Dark2")))
checkException(plotOneFit(tcga_mm, "NOTAGENE", brewer.pal(n = 4, name = "Dark2")))
checkException(plotOneFit(tcga_mm, "NOTAGENE", brewer.pal(n = 3, name = "Dark2")))
#########################################################################
#Test plotMarginals()
#########################################################################
checkException(plotMarginals(1, "average", brewer.pal(n = 4, name = "Dark2")))
checkException(plotMarginals(fit, "publishability", brewer.pal(n = 4, name = "Dark2")))
checkException(plotMarginals(fit, "average", brewer.pal(n = 3, name = "Dark2")))
#########################################################################
#Test plotMostDiscordant()
#########################################################################
checkException(plotMostDiscordant(1, "sensitivity", 15))
checkException(plotMostDiscordant(fit, "publishability", 15))
checkException(plotMostDiscordant(fit, "sensitivity", -2))
#########################################################################
}
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