segments.summary: Additional summary measured for the segments

In DNAcopy: DNA copy number data analysis

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.

Author(s)

Venkatraman E. Seshan

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)

DNAcopy documentation built on Nov. 8, 2020, 5:48 p.m.