sigora: Signature Overrepresentation Analysis

Pathway Analysis is the process of statistically linking observations on the molecular level to biological processes or pathways on the systems (organism, organ, tissue, cell) level. Traditionally, pathway analysis methods regard pathways as collections of single genes and treat all genes in a pathway as equally informative. This can lead to identification of spurious (misleading) pathways as statistically significant, since components are often shared amongst pathways. SIGORA seeks to avoid this pitfall by focusing on genes or gene-pairs that are (as a combination) specific to a single pathway. In relying on such pathway gene-pair signatures (Pathway-GPS), SIGORA inherently uses the status of other genes in the experimental context to identify the most relevant pathways. The current version allows for pathway analysis of human and mouse data sets and contains pre-computed Pathway-GPS data for pathways in the KEGG and Reactome pathway repositories as well as mechanisms for extracting GPS for user supplied repositories.

Author
Amir B.K. Foroushani, Fiona S.L. Brinkman, David J. Lynn
Date of publication
2016-05-11 00:26:37
Maintainer
Amir Foroushani <sigora.dev@gmail.com>
License
GPL-2
Version
2.0.1

View on CRAN

Man pages

genesFromRandomPathways
Function to randomly select genes associated with randomly...
getGenes
List genes involved in present GPS for a specific pathway in...
idmap
Identifier mappings for protein coding genes.
kegH
Pathway GPS data, extracted from KEGG repository (Human).
kegM
Pathway GPS data, extracted from KEGG repository (Mouse).
makeGPS
Create your own Signature Object.
nciTable
NCI human gene-pathway associations.
ora
Traditional Overrepresentation Analysis.
reaH
Pathway GPS data, extracted from the Reactome repository...
reaM
Pathway GPS data, extracted from Reactome repository (Mouse).
sigora
Sigora's main function.
sigora-package
SIGNATURE OVERREPRESENTATION ANALYSIS

Files in this package

sigora
sigora/inst
sigora/inst/CITATION
sigora/NAMESPACE
sigora/data
sigora/data/idmap.rda
sigora/data/nciTable.rda
sigora/data/reaM.rda
sigora/data/kegM.rda
sigora/data/datalist
sigora/data/kegH.rda
sigora/data/reaH.rda
sigora/R
sigora/R/makeGPS.R
sigora/R/genesFromRandomPathways.R
sigora/R/getGenes.R
sigora/R/ora.R
sigora/R/sigora.R
sigora/MD5
sigora/DESCRIPTION
sigora/man
sigora/man/getGenes.Rd
sigora/man/makeGPS.Rd
sigora/man/nciTable.Rd
sigora/man/sigora.Rd
sigora/man/reaM.Rd
sigora/man/idmap.Rd
sigora/man/genesFromRandomPathways.Rd
sigora/man/kegH.Rd
sigora/man/reaH.Rd
sigora/man/kegM.Rd
sigora/man/sigora-package.Rd
sigora/man/ora.Rd