dataDART: Example data for DART package

In DART: Denoising Algorithm based on Relevance network Topology

Description

This data object consists of a gene expression data matrix over 67 oestrogen receptor negative breast cancers (Wang, Y. et al. Lancet 365, 671-9 (2005)), of which 51 are basals and 16 are HER2+/ERBB2+. This classification is based on the intrinsic subtype classifier (see Hu Z, et al., BMC Genomics. 2006 Apr 27;7:96), and while not equivalent to IHC or the amplification status at the ERBB2 locus, it broadly matches these other classifications. The model pathway signature is an in-vitro derived perturbation signature reflecting ERBB2 activation (see Creighton CJ, et al., Cancer Res 2006 Apr 1;66(7):3903-11). Both data and signature are annotated with Entrez Gene IDs.

Usage

dataDART

Format

A list with 4 elements: (i) data: is the gene expression matrix described above, (ii) sign: is the ERBB2 perturbation signature, (iii) pheno: basal/ERBB2 status of samples, (iv) phenoMAINZ: basal/ERBB2 status of a further set of samples.

Examples

data(dataDART)
names(dataDART)

DART documentation built on Nov. 8, 2020, 5:06 p.m.