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'))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(lol)
Loading required package: penalized
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lol/chin07.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chin07
> ### Title: Breast cancer data set of genome-wide copy number merged data
> ###   and expression of some important genes
> ### Aliases: chin07
> ### Keywords: datasets
> 
> ### ** 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'))
png 
  2 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>