ratexample: Example of copy number log ratio data

In CNprep: Pre-Process DNA Copy Number (CN) Data for Detection of CN Events

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.

Source

Genome Res. 2006 Dec;16(12):1465-79.

Novel patterns of genome rearrangement and their association with survival in breast cancer.

Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E, Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye K, Borresen-Dale AL, Naume B, Schlicting E, Norton L, Hagerstrom T, Skoog L, Auer G, Maner S, Lundin P, Zetterberg A.

Examples

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])

CNprep documentation built on May 24, 2022, 5:05 p.m.