knownSignatures: Previously identified gene signatures for use in...

In SigCheck: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

Description

Previously identified gene signature sets. These include three signatures sets from Venet et. al.

Usage

data(knownSignatures)

Format

The data object knownSignatures is a list of sets of gene signatures. Each set is a list of gene signatures. Each signature is a vector of gene names.

Gene signature sets include:

• "cancer": 48 gene signatures derived from cancer samples, from Venet et. al.

• "proliferation": 5 gene signatures comprising genes associated with cell proliferation, including a "super signature", from Venet et. al.

• "non.cancer": 3 gene signatures derived from non-cancer sources, from Venet et. al.

Details

These data are taken directly from the supplemental material for Venet et. al "Most random gene expression signatures are significantly associated with breast cancer outcome".

Note

Other signatures of interest can be downloaded at http://www.broad.mit.edu/gsea/downloads.jsp#msigdb and read in using the read.gmt function in the qusage package.

Source

http://www.ploscompbiol.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pcbi.1002240.s001

References

Venet, David, Jacques E. Dumont, and Vincent Detours. "Most random gene expression signatures are significantly associated with breast cancer outcome." PLoS Computational Biology 7.10 (2011): e1002240.

Examples

data(knownSignatures)
names(knownSignatures)
names(knownSignatures$cancer)
knownSignatures$cancer$VANTVEER

SigCheck documentation built on Nov. 8, 2020, 6:38 p.m.