R: Breast cancer gene expression + DNA copy number data set from...

breastdata {PMA} | R Documentation

## Breast cancer gene expression + DNA copy number data set from Chin et. al. and used in Witten, et. al. See references below.

### Description

This data set consists of gene expression and DNA copy number measurements on a set of 89 samples. The data set can be used to perform integrative analysis of gene expression and DNA copy number data, as in . That is, we can look for sets of genes that are associated with regions of chromosomal gain/loss.

Must be downloaded from https://statweb.stanford.edu/~tibs/PMA/ and put into the folder PMA/data

### Format

The format is a list containing the following elements: - dna: a 2149x89 matrix of CGH spots x Samples - rna: a 19672x89 matrix of Genes x Samples - chrom: a 2149-vector of chromosomal location of each CGH spot - nuc: a 2149-vector of nucleotide position for each CGH spot - gene: a 19672-vector wiith an accession number for each gene - genenames: a 19672-vector with a name for each gene - genechr: a 19672-vector with a chromosomal location for each gene - genedesc: a 19672-vector with a description for each gene - genepos: a 19672-vector with a nucleotide position for each gene

### Details

Missing values were imputed using 5-nearest neighbors (see library `pamr`).

### References

Chin K., et. al. (2006) doi: 10.1016/j.ccr.2006.10.009.

Witten D. M., Tibshirani R., and Hastie, T. (2009) doi: 10.1093/biostatistics/kxp008.

### Examples

    ## Not run:
    data(breastdata)
    attach(breastdata)
    PlotCGH(dna[,1], chrom=chrom, main="Sample 1", nuc=nuc)
    detach(breastdata)

    ## End(Not run)

[Package PMA version 1.2.1 Index]