tcga2012brca: Sample breast cancer data from TCGA
In achambaz/tmle.npvi: Targeted Learning of a NP Importance of a Continuous Exposure

Description Usage Format Details Author(s) Source References Examples

Expression, DNA copy number, and DNA methylation data of 125 genes of chromosome 17 for 463 breast cancer samples from TCGA.

1	tcga2012brca

A list of matrices. Each matrix corresponds to a particular gene and has the following columns:

Y: gene expression level (outcome variable)
X: DNA copy number (continuous exposure variable)
W1 … Wk: DNA methylation (k baseline covariates)

These data were obtained using the scripts located in testScripts/tcga2012brca. See the tmle-npvi.pdf vignette for more details on the preparation of the data set.

Gene names and genomic coordinates are stored in the names of the list.

Antoine Chambaz, Pierre Neuvial

Raw data may be retrieved from https://tcga-data.nci.nih.gov/docs/publications/brca_2012/

methylation: http://tcga-data.nci.nih.gov/docs/publications/brca_2012/BRCA.methylation.27k.450k.466.zip
copy number data: http://tcga-data.nci.nih.gov/docs/publications/brca_2012/BRCA.GISTIC2.tar.gz
expression: http://tcga-data.nci.nih.gov/docs/publications/brca_2012/BRCA.exp.466.med.txt
annotation data for methylation probes: https://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit/downloads.html

Chambaz, A., Neuvial, P., & van der Laan, M. J. (2012). Estimation of a non-parametric variable importance measure of a continuous exposure. Electronic journal of statistics, 6, 1059–1099.

Cancer Genome Atlas Network. (2012). Comprehensive molecular portraits of human breast tumours. Nature, 490(7418), 61-70.

  data(tcga2012brca)
  nms <- names(tcga2012brca)
  ii <- grep("TP53", nms)
  obs <- tcga2012brca[[ii]]
  pairs(obs, main=nms[ii])

  thr <- 0.02
  whichSmall <- which(abs(obs[, "X"]) <= thr)
  obs[whichSmall, "X"] <- 0

  ## the code below takes ~20s to run
  ## Not run: res <- tmle.npvi(obs)