rstats-test

Binary Segmentation Project tests

Easy

• Download data(neuroblastoma, package=”neuroblastoma”) and plot profile.id=4, chromosome=2, (y=logratio, x=position).

  total data points = 234
  

  

• Use binsegRcpp to compute binary segmentation models up to 5 segments (change in mean, normal distribution), then plot those segment means and changepoints on top of the data.

  S No.	1	2	3	4	5	6
  Segment	1-41	42-113	114-146	147-152	153-157	158-234
  Mean	0.351231083	0.005885206	-0.447813047	-0.307411681	-0.666259257	0.003035709
  Changepoint	41	113	146	152	157	-

  

Medium

• Use the changepoint package to compute models up to 5 segments for the same data set.

  S No.	1	2	3	4	5	6
  Segment	1-41	42-113	114-152	153-157	158-220	220-234
  Mean	0.351231083	0.005885206	-0.426212837	-0.666259257	0.016075375	-0.055642790
  Changepoint	41	113	152	157	220	-

• Are the changepoints the same?

  While most of the changepoints are same there are few variation, shown in table and in figure as blue box.

  Package	Changepoints
  binsegRcpp	41	113	146	152	157
  changepoint	41	113	152	157	220

  

Hard 1

• Implement Negative Binomial loss function in C code using the same arguments as in changepoint/src/cost_general_functions.c.

Hard 2

• Fork binsegRcpp and modify src/binseg_normal.cpp so that it computes change in mean and variance (instead of change of mean with constant variance).
• Use it to compute changepoints for the same neuroblastoma data set, and verify that the result is the same as the result of changepoint::cpt.meanvar.