cgps

0th

Percentile

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

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

Keywords
datasets
Usage
data(cgps)
Details

Camptothecin is a drug mainly used in colorectal cancer.

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

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.

Aliases
  • cgps.annot
  • cgps.ge
  • cgps.ic50
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))
Documentation reproduced from package mRMRe, version 2.0.5, License: Artistic-2.0

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