dat: A test dataset for the RTopper package

In RTopper: This package is designed to perform Gene Set Analysis across multiple genomic platforms

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)

RTopper documentation built on Nov. 8, 2020, 5:08 p.m.