R: Part of the large pharmacogenomic dataset published by...

cgps {mRMRe} | R Documentation

## Part of the large pharmacogenomic dataset published by Garnett et al. within the Cancer Genome Project (CGP)

### Description

This dataset contains gene expression of 200 cancer cell lines for which sensitivity (IC50) to Camptothecin was measured (release 2).

### Usage

    data(cgps)

### Format

The `cgps` dataset is composed of three objects

cgps.annot

  Dataframe containing gene annotations

cgps.ge

  Matrix containing expressions of 1000 genes; cell lines in rows, genes in columns

cgps.ic50

  Drug sensitivity measurements (IC50) for Camptothecin

### Details

Camptothecin is a drug mainly used in colorectal cancer.

### Source

http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-783

http://www.nature.com/nature/journal/v483/n7391/extref/nature11005-s2.zip

### References

Garnett MJ et al. "Systematic identification of genomic markers of drug sensitivity in cancer cells", Nature, 483:570-575, 2012.

### Examples

    set.thread.count(2)
    data(cgps)

    message("Gene expression data:")
    print(cgps.ge[1:3, 1:3])

    message("Gene annotations:")
    print(head(cgps.annot))

    message("Drug sensitivity (IC50) values:")
    print(head(cgps.ic50))

[Package mRMRe version 2.0.9 Index]