mirror of
https://github.com/avinal/rstats-test.git
synced 2026-01-11 15:48:33 +05:30
44 lines
1.2 KiB
R
44 lines
1.2 KiB
R
|
# 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()
|