Task 2 completed

Medium/task2.r

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+# Using changepoint to compute binary segmentation models up to 5 segments
+# Plot segement means on top of data
+
+if(!require(changepoint)) {
+    install.packages("changepoint")
+}
+
+if(!require(neuroblastoma)) {
+    install.packages("neuroblastoma")
+}
+
+# import and load neuroblastoma dataset
+library('neuroblastoma')
+data('neuroblastoma')
+
+# using np as neuro.profiles for profile data
+np = neuroblastoma$profiles
+xy = np[np$profile.id == 4 & np$chromosome == 2, ]
+x = xy$position
+y = xy$logratio
+
+# calculate changepoints
+model <- changepoint::cpt.meanvar(y,penalty="Manual",pen.value='2*log(n)',method='BinSeg', Q=10)
+cm = coef(model)
+change.points = cpts(model)
+segment.mean = cm[1]
+
+# detected changepoints
+print(change.points)
+
+# segment means
+print(segment.mean)
+
+# plot changepoint and segment mean over data
+svg('Medium/task2.svg')
+plot(model, xlab="Segments", ylab="logpoint ratios of the probe", main="Neuroblastoma changepoint detection using 'changepoint'")
+grid()
+legend(x=5, y=-0.5,legend=c("position vs logpoint data", "segment mean", "changepoint"), col=c("black","red","blue"), lty=c(1,1,NA), pch=c(NA,NA,'X'), cex=0.8, bg='lightblue')
+
+# add changepoints
+points(change.points, as.numeric(segment.mean[[1]])[1:5], col='blue', pch='X')
+
+dev.off()