CNprep (version 2.2)

ratexample: Example of copy number log ratio data

Description

Log ratio data for 5 breast cancer genomes, derived using Representational Oligonucleotide Microarray Analysis (ROMA), an array-based hybridization method that uses genomic complexity reduction based on representations.

Usage

data(ratexample)

Format

A log ratio data matrix with rows of 83055 oligonucleotide probes, and columns of 5 breast tumors.

Details

The values are natural log copy number ratios, consistent with data in segexample (segmented data for these tumors) and normsegs. These copy number ratios are normalized using an intensity-based lowess curve fitting algorithm.

Examples

# NOT RUN {
data(ratexample)
#Plot the whole genome log ratio data for the first profile 
#Note X and Y chromosomes at the far  right of the plot
plot(ratexample[,1])
# }