crcTCGAsubset: colorectal TCGA gene expression data with subtype annotation

In peterawe/CMScaller: CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Description

The Cancer Genome Atlas level 3 RSEM genes data was retrieved from Broad GDAC Firehose, doi:10.7908/C11G0KM9 (http://gdac.broadinstitute.org/). Samples were annotated with Consensus Molecular Subtypes (Guinney 2015), Sadanandam subtypes (Isella 2015) and ABSOLUTE estimated tumor purity (Aran 2015). Features were annotated using fromTo. Rownames are Entrez ids. Included are 92 HiSeq test set samples with genes with maximum count exceeding 25.

Usage

crcTCGAsubset

Format

An object of class ExpressionSet with 16863 rows and 92 columns.

References

Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015;6:8971.

Guinney J, Dienstmann R, Wang X, de Reynies A, Schlicker A, Soneson C, et al. The consensus molecular subtypes of colorectal cancer. Nat Med. 2015;21:1350-6.

Isella C, Terrasi A, Bellomo SE, Petti C, Galatola G, Muratore A, et al. Stromal contribution to the colorectal cancer transcriptome. Nat Genet [Internet]. 2015 [cited 2015 Mar 2];advance online publication. Available from: http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3224.html

TCGA. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330-7.

Examples

library(Biobase)
dim(crcTCGAsubset)

peterawe/CMScaller documentation built on June 13, 2020, 4:49 a.m.