R/download_breast_data.R

In PMA: Penalized Multivariate Analysis

#' Download and return the breast data
#'
#' @description
#' 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`).
#' @param url source, default `"https://tibshirani.su.domains/PMA/breastdata.rda"`
#' @return 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.
#' @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}.
#' @importFrom utils download.file
#' @export download_breast_data
download_breast_data <- function(url = "https://tibshirani.su.domains/PMA/breastdata.rda") {
  tmpdir <- tempdir()
  filepath <- file.path(tmpdir, "breastdata.rda")
  utils::download.file(url, filepath)
  e <- new.env()
  load(filepath, envir = e)
  e$breastdata
}