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### R code from vignette source 'nlcv.Rnw'
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### code chunk number 1: init
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if(!dir.exists("./graphs")) dir.create("./graphs")
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### code chunk number 2: Setting
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options(width=65)
set.seed(123)
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### code chunk number 3: LoadLib
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library(nlcv)
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### code chunk number 4: Simulation
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EsetRandom <- simulateData(nCols = 40, nRows = 1000, nEffectRows = 0, nNoEffectCols = 0)
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### code chunk number 5: Simulation
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EsetStrongSignal <- simulateData(nCols = 40, nRows = 1000, nEffectRows = 10,
nNoEffectCols = 0, betweenClassDifference = 3, withinClassSd = 0.5)
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### code chunk number 6: Simulation
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EsetWeakSignal <- simulateData(nCols = 40, nRows = 1000, nEffectRows = 5,
nNoEffectCols = 0, betweenClassDifference = 1, withinClassSd = 0.6)
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### code chunk number 7: Simulation
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EsetStrongHeteroSignal <- simulateData(nCols = 40, nRows = 1000, nEffectRows = 5,
nNoEffectCols = 5, betweenClassDifference = 3, withinClassSd = 0.5)
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### code chunk number 8: Simulation
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EsetWeakHeteroSignal <- simulateData(nCols = 40, nRows = 1000, nEffectRows = 5,
nNoEffectCols = 5, betweenClassDifference = 1, withinClassSd = 0.6)
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### code chunk number 9: Simulation
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geneX <- 1
myData <- EsetStrongHeteroSignal
xx <- pData(myData)$type
yy <- exprs(myData)[geneX,]
myTitle <- rownames(exprs(myData))[geneX]
pdf(file = "./graphs/plotGeneSHS.pdf")
boxplot(yy~xx,col='grey',xlab='',ylab='', main = myTitle, axes=FALSE)
text(xx,yy,labels=colnames(exprs(myData)),col='blue',pos=4,cex=0.7)
axis(1, at=1:2, labels=levels(xx));axis(2, las=2)
dev.off()
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### code chunk number 10: nlcv (eval = FALSE)
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## nlcvTT_SS <- nlcv(EsetStrongSignal, classVar = "type", nRuns = 2,
## fsMethod = "t.test", verbose = TRUE)
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### code chunk number 11: nlcv load_objects_20runs
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# No Signal - Random data
data("nlcvRF_R"); data("nlcvTT_R")
# Strong Signal
data("nlcvRF_SS"); data("nlcvTT_SS")
# Weak Signal
data("nlcvRF_WS"); data("nlcvTT_WS")
# Strong, heterogeneous Signal
data("nlcvRF_SHS"); data("nlcvTT_SHS")
# Weak, heterogeneous Signal
data("nlcvRF_WHS"); data("nlcvTT_WHS")
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### code chunk number 12: nlcv run_objects_20runs
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# # Sidenote: nlcvRF_SS (loaded in the previous chunk) was obtained with following code
# nlcvRF_SS <- nlcv(EsetStrongSignal, classVar = "type", nRuns = 20, fsMethod = "randomForest", verbose = TRUE)
# save(nlcvRF_SS, file = "nlcvRF_SS.rda")
# nlcvTT_SS <- nlcv(EsetStrongSignal, classVar = "type", nRuns = 20, fsMethod = "t.test", verbose = TRUE)
# save(nlcvTT_SS, file = "nlcvTT_SS.rda")
#
# Similarly for any other dataset, like EsetWeakSignal, WeakHeteroSignal, StrongHeteroSignal and EsetRandom
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### code chunk number 13: mcrPlot_RandomData
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# plot MCR versus number of features
pdf(file = "./graphs/mcrPlot_nlcv_R.pdf", width = 10, height = 5)
layout(matrix(1:4, ncol = 2), height = c(6, 1, 6, 1))
mcrPlot_RF_R <- mcrPlot(nlcvRF_R, plot = TRUE, optimalDots = TRUE,
layout = FALSE, main = 'RF selection')
mcrPlot_TT_R <- mcrPlot(nlcvTT_R, plot = TRUE, optimalDots = TRUE,
layout = FALSE, main = 'T selection')
layout(1)
dev.off()
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### code chunk number 14: scoresPlot_RandomData
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pdf(file = "./graphs/ScoresPlot_nlcv_R.pdf", width = 10, height = 6)
scoresPlot(nlcvRF_R, "randomForest", 5)
dev.off()
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### code chunk number 15: selGenes
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outtable <- topTable(nlcvRF_R, n = 10)
xtable(outtable, label = "tab:selGenes_R",
caption="Top 10 features across all runs of the nested loop cross-validation.")
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### code chunk number 16: Simulation
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geneX <- 1
myData <- EsetStrongSignal
xx <- pData(myData)$type
yy <- exprs(myData)[geneX,]
myTitle <- rownames(exprs(myData))[geneX]
pdf(file = "./graphs/plotGeneSS.pdf")
boxplot(yy~xx,col='grey',xlab='',ylab='', main = myTitle, axes=FALSE)
text(xx,yy,labels=colnames(exprs(myData)),col='blue',pos=4,cex=0.7)
axis(1, at=1:2, labels=levels(xx));axis(2, las=2)
dev.off()
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### code chunk number 17: RandomData
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# plot MCR versus number of features
pdf(file = "./graphs/mcrPlot_nlcv_SS.pdf", width = 10, height = 5)
layout(matrix(1:4, ncol = 2), height = c(6, 1, 6, 1))
mcrPlot_SSF_SS <- mcrPlot(nlcvRF_SS, plot = TRUE, optimalDots = TRUE, layout = FALSE, main = 'RF selection')
mcrPlot_TT_SS <- mcrPlot(nlcvTT_SS, plot = TRUE, optimalDots = TRUE, layout = FALSE, main = 'T selection')
dev.off()
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### code chunk number 18: RandomData
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pdf(file = "./graphs/ScoresPlot_nlcv_SS.pdf", width = 10, height = 6)
scoresPlot(nlcvRF_SS, "randomForest", 5)
dev.off()
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### code chunk number 19: selGenes
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outtable <- topTable(nlcvRF_SS, n = 12)
xtable(outtable, label = "tab:selGenes_SS",
caption="Top 20 features across all runs of the nested loop cross-validation.")
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### code chunk number 20: Simulation
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geneX <- 1
myData <- EsetWeakSignal
xx <- pData(myData)$type
yy <- exprs(myData)[geneX,]
myTitle <- rownames(exprs(myData))[geneX]
pdf(file = "./graphs/plotGeneWS.pdf")
boxplot(yy~xx,col='grey',xlab='',ylab='', main = myTitle, axes=FALSE)
text(xx,yy,labels=colnames(exprs(myData)),col='blue',pos=4,cex=0.7)
axis(1, at=1:2, labels=levels(xx));axis(2, las=2)
dev.off()
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### code chunk number 21: RandomData
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# plot MCR versus number of features
pdf(file = "./graphs/mcrPlot_nlcv_WS.pdf", width = 10, height = 5)
layout(matrix(1:4, ncol = 2), height = c(6, 1, 6, 1))
mcrPlot_WSF_WS <- mcrPlot(nlcvRF_WS, plot = TRUE, optimalDots = TRUE, layout = FALSE, main = 'RF selection')
mcrPlot_TT_WS <- mcrPlot(nlcvTT_WS, plot = TRUE, optimalDots = TRUE, layout = FALSE, main = 'T selection')
dev.off()
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### code chunk number 22: ScoresPlot_nlcv_WS
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pdf(file = "./graphs/ScoresPlot_nlcv_WS.pdf", width = 10, height = 6)
scoresPlot(nlcvRF_WS, "svm", 7)
dev.off()
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### code chunk number 23: selGenesNlcvTT_WS
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outtable <- topTable(nlcvTT_WS, n = 7)
xtable(outtable, label = "tab:selGenes_WS1",
caption="Top 20 features selected with t-test across all runs of the nested loop cross-validation.")
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### code chunk number 24: selGenesNlcvRF_WS
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outtable <- topTable(nlcvRF_WS, n = 7)
xtable(outtable, label = "tab:selGenes_WS2",
caption="Top 20 features selected with RF variable importance across all runs of the nested loop cross-validation.")
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### code chunk number 25: Simulation
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geneX <- 1
myData <- EsetStrongHeteroSignal
xx <- pData(myData)$type
yy <- exprs(myData)[geneX,]
myTitle <- rownames(exprs(myData))[geneX]
pdf(file = "./graphs/plotGeneSHS.pdf")
boxplot(yy~xx,col='grey',xlab='',ylab='', main = myTitle, axes=FALSE)
text(xx,yy,labels=colnames(exprs(myData)),col='blue',pos=4,cex=0.7)
axis(1, at=1:2, labels=levels(xx));axis(2, las=2)
dev.off()
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### code chunk number 26: mcrPlot_nlcv_SHS
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# plot MCR versus number of features
pdf(file = "./graphs/mcrPlot_nlcv_SHS.pdf", width = 10, height = 5)
layout(matrix(1:4, ncol = 2), height = c(6, 1, 6, 1))
mcrPlot_SHSF_SHS <- mcrPlot(nlcvRF_SHS, plot = TRUE, optimalDots = TRUE, layout = FALSE, main = 'RF selection')
mcrPlot_TT_SHS <- mcrPlot(nlcvTT_SHS, plot = TRUE, optimalDots = TRUE, layout = FALSE, main = 'T selection')
dev.off()
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### code chunk number 27: scoresPlots
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pdf(file = "./graphs/ScoresPlot_nlcv_SHS.pdf", width = 10, height = 6)
scoresPlot(nlcvTT_SHS, "pam", 7)
dev.off()
pdf(file = "./graphs/ScoresPlot_nlcv_SHS2.pdf", width = 10, height = 6)
scoresPlot(nlcvTT_SHS, "randomForest", 7)
dev.off()
pdf(file = "./graphs/ScoresPlot_nlcv_SHS3.pdf", width = 10, height = 6)
scoresPlot(nlcvRF_SHS, "randomForest", 7)
dev.off()
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### code chunk number 28: selGenes
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outtable <- topTable(nlcvTT_SHS, n = 7)
xtable(outtable, label = "tab:selGenes_SHS1",
caption="Top 20 features selected with t-test across all runs of the nested loop cross-validation.")
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### code chunk number 29: selGenes
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outtable <- topTable(nlcvRF_SHS, n = 7)
xtable(outtable, label = "tab:selGenes_SHS2",
caption="Top 20 features selected with RF variable importance across all runs of the nested loop cross-validation.")
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### code chunk number 30: Simulation
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geneX <- 1:4
myData <- EsetWeakHeteroSignal
xx <- pData(myData)$type
pdf(file = "./graphs/plotGeneWHS.pdf")
par(mfrow=c(2,2))
for (i in 1:4){
yy <- exprs(myData)[geneX[i],]
myTitle <- rownames(exprs(myData))[geneX[i]]
boxplot(yy~xx,col='grey',xlab='',ylab='', main = myTitle, axes=FALSE)
text(xx,yy,labels=colnames(exprs(myData)),col='blue',pos=4,cex=0.85)
axis(1, at=1:2, labels=levels(xx));axis(2, las=2)
}
par(mfrow=c(1,1))
dev.off()
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### code chunk number 31: RandomData
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# plot MCR versus number of features
pdf(file = "./graphs/mcrPlot_nlcv_WHS.pdf", width = 10, height = 5)
layout(matrix(1:4, ncol = 2), height = c(6, 1, 6, 1))
mcrPlot_WHSF_WHS <- mcrPlot(nlcvRF_WHS, plot = TRUE, optimalDots = TRUE, layout = FALSE, main = 'RF selection')
mcrPlot_TT_WHS <- mcrPlot(nlcvTT_WHS, plot = TRUE, optimalDots = TRUE, layout = FALSE, main = 'T selection')
dev.off()
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### code chunk number 32: RandomData
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pdf(file = "./graphs/ScoresPlot_nlcv_WHS.pdf", width = 10, height = 6)
scoresPlot(nlcvTT_WHS, "pam", 2)
dev.off()
pdf(file = "./graphs/ScoresPlot_nlcv_WHS0.pdf", width = 10, height = 6)
scoresPlot(nlcvTT_WHS, "pam", 10)
dev.off()
pdf(file = "./graphs/ScoresPlot_nlcv_WHS2.pdf", width = 10, height = 6)
scoresPlot(nlcvTT_WHS, "randomForest", 15)
dev.off()
pdf(file = "./graphs/ScoresPlot_nlcv_WHS3.pdf", width = 10, height = 6)
scoresPlot(nlcvRF_WHS, "randomForest", 5)
dev.off()
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### code chunk number 33: selGenes
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outtable <- topTable(nlcvTT_WHS, n = 10)
xtable(outtable, label = "tab:selGenes_WHS1",
caption="Top 20 features selected with t-test across all runs of the nested loop cross-validation.")
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### code chunk number 34: selGenes
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outtable <- topTable(nlcvRF_WHS, n = 10)
xtable(outtable, label = "tab:selGenes_WHS2",
caption="Top 20 features selected with RF variable importance across all runs of the nested loop cross-validation.")
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### code chunk number 35: sessionInfo
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toLatex(sessionInfo())
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