ctrp2: Processed Cancer Cell Line Encyclopedia (CCLE) and Cancer...

In hierBipartite: Bipartite Graph-Based Hierarchical Clustering

Description

Smaller test dataset version of the "CTRP2" carcinoma dataset in the paper. Specifically, only the top 1,000 transcripts by correlation with drug sensitivity are included instead of 5,000. Otherwise the dataset has been processed exactly as described in the paper. Note the expression dataset is provided by CCLE and the drug sensitivity dataset is provided by CTRP2, and the pharmacogenomic datasets in the paper are are referred to by the resource providing the sensitivity data. The cell lines are grouped by carcinoma subtype and primary site (e.g. lung NSC).

Usage

data(ctrp2)

Format

A list with elements of gene expression, drug sensitivities, and group membership.

X

n x p gene expression matrix

Y

n x q drug sensitivities matrix

groups

List of starting groups. Each group is represented by a vector of row indices for X, Y.

References

Barretina, J., et al. (2012). The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature, 483(7391), 603–607. (PubMed)

Seashore-Ludlow, B., et al. (2015). Harnessing connectivity in a large-scale small-molecule sensitivity dataset. Cancer discovery, 5(11), 1210-1223. (PubMed)

Examples

data(ctrp2)
X = ctrp2[["X"]]
Y = ctrp2[["Y"]]
groups = ctrp2[["groups"]]

hierBipartite documentation built on Feb. 16, 2021, 5:07 p.m.