tcga2012brca: Sample breast cancer data from TCGA

In tmle.npvi: Targeted Learning of a NP Importance of a Continuous Exposure

Description

Expression, DNA copy number, and DNA methylation data of 125 genes of chromosome 21 for 463 breast cancer samples from TCGA.

Usage

tcga2012brca

Format

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)

Details

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.

Author(s)

Antoine Chambaz, Pierre Neuvial

Source

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

http://supportres.illumina.com/documents/myillumina/b78d361a-def5-4adb-ab38-e8990625f053/humanmethylation450_15017482_v1-2.csv

References

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.

Examples

  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)

Example output

Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save

R.utils v2.8.0 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings

tmle.npvi documentation built on May 1, 2019, 6:50 p.m.