relCNComp {seqCBS} | R Documentation |
This computes the relative copy number by each of the segment called
relCNComp(combX, combZ, tauHatInd, p, alpha)
combX |
The number of reads at each unique read position |
combZ |
The number of case/tumor reads at each unique read position |
tauHatInd |
The index of change points called |
p |
The overall proportion of case reads |
alpha |
Significance level for testing whether each segment is a gain (relative CN > 1) or loss (relative CN < 1). The method internally corrects for multiple testing. |
The relative CN is defined as the number of case reads divided by the number of control reads in a window, adjusted for overall proportion of case reads (divided by the overall relative CN).
Returns a vector of relative CN for each of the segment between two change points
Jeremy J. Shen