Breast cancer gene expression + DNA copy number data set from Chin et. al. and used in Witten, et. al. See references below.
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.
Missing values were imputed using 5-nearest neighbors (see library
pamr).
download_breast_data(url = "https://tibshirani.su.domains/PMA/breastdata.rda")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.
source, default "https://tibshirani.su.domains/PMA/breastdata.rda"
Chin K., et. al. (2006) tools:::Rd_expr_doi("10.1016/j.ccr.2006.10.009").
Witten D. M., Tibshirani R., and Hastie, T. (2009) tools:::Rd_expr_doi("10.1093/biostatistics/kxp008").