segments.p {DNAcopy} | R Documentation |
This program computes a p-value for the change-points found by the circular binary segmentation (CBS) algorithm.
segments.p(x, ngrid=100, tol=1e-6)
x |
an object of class DNAcopy |
ngrid |
number grid points for the integral |
tol |
tolerance level for calculating nu |
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.
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.
Venkatraman E. Seshan olshena@mskcc.org
# 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)