lol (version 1.20.0)

chin07: Breast cancer data set of genome-wide copy number merged data and expression of some important genes

Description

A subset of breast cancer data as used in Yuan et al. (to be submitted).

Usage

data(chin07)

Format

A list object of two named data matrices, cn: DNA copy number, ge: RNA expression. The matrices columns are samples and rows are probes/variables.

Details

Genome-wide copy number data was merged using CGHregions resulting in 339 regions across 106 samples. Expression data are 7 probes mapped to important breast cancer genes such as CCNE2, MYC, etc, also of 106 samples.

References

Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, et al. (2007) High-resolution arraycgh and expression profiling identifies a novel genomic subtype of er negative breast cancer. Genome Biology 8: R215+. Yuan et al. (2011) Discovery and functional annotation of cis- and trans-acting DNA copy number hotspots in breast cancer, to be submitted.

Examples

data(chin07)
gain <- rowSums(chin07$cn >= .2)
loss <- -rowSums(chin07$cn <= -.2)
plotGW(data=cbind(gain, loss), pos=attr(chin07$cn, 'chrome'), legend=c('gain', 'loss'))