cgps {mRMRe}

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))