annotationListToMatrix

gene2set

a gmt file. Examples are from MSigDB Collections.
A list of gene set could be find in the vignette of cogena

annofile

genenames

a threshold for the Term Frequence. Default is zero.

TermFreq

a value returned by <code><a rd-options="" href="/link/gmt2list?package=cogena&version=1.6.2" data-mini-rdoc="cogena::gmt2list">gmt2list</a></code>.

annotation


Generate relationship between genes (gene SYMBOL) and gene-sets, 
such as Pathway or GO.


cogena is a workflow for co-expressed gene-set enrichment analysis.
It aims to discovery smaller scale, but highly correlated cellular events that
may be of great biological relevance. A novel pipeline for drug discovery and
drug repositioning based on the cogena workflow is proposed. Particularly,
candidate drugs can be predicted based on the gene expression of disease-related
data, or other similar drugs can be identified based on the gene expression
of drug-related data. Moreover, the drug mode of action can be disclosed by
the associated pathway analysis. In summary, cogena is a flexible workflow for
various gene set enrichment analysis for co-expressed genes, with a focus on
pathway/GO analysis and drug repositioning.

gene2set: generate relationship between genes and gene-sets

Description

Usage

Arguments

Value

Examples