View source: R/pathwayanalysis.R
pathwayanalysis | R Documentation |
Run Overrepresentation Analysis via the ClusterProfiler workflow
pathwayanalysis(sigres, term2gene)
sigres |
data.frame of significant genes. first column is gene names; second column is logfoldchange or other effect size. |
term2gene |
data.frame of pathways to check. first column is pathways, second column is genes. |
a list object: first element is a ClusterProfiler object; second element is an "emap plot", a graph of pathways connected by jaccard similarity; third element is a data.frame with the connected nodes from the emap plot; 4th element is a list of pathways in each connected cluster; 5th element is genes from the pathways in each cluster
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