ratexample {CNprep}R Documentation

Example of copy number log ratio data


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.




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


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.


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.


#Plot the whole genome log ratio data for the first profile 
#Note X and Y chromosomes at the far  right of the plot

[Package CNprep version 2.2 Index]