dat {RTopper} | R Documentation

## A test dataset for the RTopper package

### Description

A small subset of pre-processed Glioblasoma Multiforme (GBM) genomic data from The Cancer Genome Atlas (TCGA) project, encompassing Differential Gene Expression (DGE), and Copy Number Variation (CNV). Can be used as input to `convertToDr`.

### Usage

     data(exampleData)

### Format

This object is a `list` of 4 `data.frames` containing genomic measurements obtained across distinct genomic scopes (copy number variation and gene expression), platforms (Affymetrix and Agiles), and laboratories. In particular each `data.frame` consist of 500 gene measurements (by rows), for 95 distinct patients (by columns) from the following 4 distinct platforms:

`"dat.affy"`: DGE obtained using Affymetrix microarrays;

`"dat.agilent"`: DGE obtained using Agilent microarrays;

`"dat.cnvHarvard"`: CNV data obtained at Harvard;

`"dat.cnvMskcc"`: CNV data obtained at Memorial Sloan Ketterng Cancer Center;

### Source

The Cancer Genome Atlas (TCGA) project http://cancergenome.nih.gov/

### References

The Cancer Genome Atlas (TCGA) Research Network. “Comprehensive genomic characterization defines human glioblastoma genes and core pathways”. Nature, 2008, October 23; 455(7216): 1061-1068

### Examples

    data(exampleData)
    ls()
    class(dat)
    names(dat)
    sapply(dat,class)
    sapply(dat,dim)

[Package RTopper version 1.40.1 Index]