segments.p {DNAcopy}R Documentation

p-values for the change-points

Description

This program computes a p-value for the change-points found by the circular binary segmentation (CBS) algorithm.

Usage

  segments.p(x, ngrid=100, tol=1e-6)

Arguments

x an object of class DNAcopy
ngrid number grid points for the integral
tol tolerance level for calculating nu

Details

The p-values are obtained by applying Siegmund's approximation for the maximal statistic from binary segmenting consecutive segments within a chromosome. This p-value is only to give the relative importance of the change-points as the CBS is different from the algorithm used here.

Value

a data frame with eight columns. The seventh column is the maximal statistic from binary segmentation and eighth is the p-values added to the six columns from the segment command.

Author(s)

Venkatraman E. Seshan olshena@mskcc.org

Examples


# test code on an easy data set
set.seed(25)
genomdat <- rnorm(500, sd=0.1) +
rep(c(-0.2,0.1,1,-0.5,0.2,-0.5,0.1,-0.2),c(137,87,17,49,29,52,87,42))
plot(genomdat)
chrom <- rep(1:2,c(290,210))
maploc <- c(1:290,1:210)
test1 <- segment(CNA(genomdat, chrom, maploc))
segments.p(test1)


[Package DNAcopy version 1.12.0 Index]