segments.summary: Additional summary measured for the segments

In veseshan/DNAcopy: DNA Copy Number Data Analysis

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.

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)

veseshan/DNAcopy documentation built on Oct. 18, 2023, 8:30 p.m.