relCNComp: Compute the Relative Copy Number

In seqCBS: Copy Number Profiling using Sequencing and CBS

Description

This computes the relative copy number by each of the segment called

Usage

relCNComp(combX, combZ, tauHatInd, p, alpha)

Arguments

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.

Details

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).

Value

Returns a vector of relative CN for each of the segment between two change points

Author(s)

Jeremy J. Shen

seqCBS documentation built on May 2, 2019, 9:15 a.m.