ScanStatRefineComp {seqCBS} | R Documentation |
This is a wrapper function to call the C routines for the scan statistic to refine current candidate segmentations computing from the IGS
ScanStatRefineComp(combZCumSum, combXCumSum, combZPoint, combXPoint, p, nTotal, grid.cur, grid.LR, max.win, statistic)
combZCumSum |
A cumulative sum of the number of case reads |
combXCumSum |
A cumulative sum of the number of reads |
combZPoint |
The number of case reads at the grid points |
combXPoint |
The number of reads at the grid points |
p |
The proportion of case reads in the current region |
nTotal |
The total number of reads in the current region |
grid.cur |
The current grid to be computed on |
grid.LR |
The left and right limits of the existing candidate segmentations that will be refined, indexed by the current grid |
max.win |
The maximum inter-window to be considered for new scan |
statistic |
The type of statistic. Can be 'binomial','rabinowitz' or 'normal'. |
The computations are done in C for speed. The three types of statistics are by the use of exact binomial likelihood ('binomial'), score statistic ('rabinowitz') or using normal approximation to the binomial ('normal').
Returns a matrix containing the refined candidate change points
Jeremy J. Shen