DNAcopy (version 1.46.0)

segments.summary: Additional summary measured for the segments

Description

This program computes the standard deviation, median and the mad of the data for each segment found by the CBS algorithm.

Usage

segments.summary(x)

Arguments

x

an object of class DNAcopy

Value

a data frame with nine columns. The sd, median and mad of each segment is added to the six columns from the segment command.

Examples

# test code on an easy data set
set.seed(25)
genomdat1 <- 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))
genomdat2 <- 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))
genomdat1[sample(1:500,5)] <- NA
chrom <- rep(1:2,c(290,210))
maploc <- c(1:290,1:210)
test1 <- segment(CNA(cbind(genomdat1,genomdat2), chrom, maploc))
segments.summary(test1)