used for integrative analysis as well as general pathways analysis for meta-analysis results
UpdateIntegPathwayAnalysis(mSetObj=NA, qids, file.nm, topo="dc", enrich="hyper", libOpt="integ")Input name of the created mSet Object
Input the query IDs
Input the name of the file
Select the mode for topology analysis: Degree Centrality ("dc") measures the number of links that connect to a node (representing either a gene or metabolite) within a pathway; Closeness Centrality ("cc") measures the overall distance from a given node to all other nodes in a pathway; Betweenness Centrality ("bc")measures the number of shortest paths from all nodes to all the others that pass through a given node within a pathway.
Method to perform over-representation analysis (ORA) based on either hypergenometrics analysis ("hyper") or Fisher's exact method ("fisher").
Select the different modes of pathways, either the gene-metabolite mode ("integ") which allows for joint-analysis and visualization of both significant genes and metabolites or the gene-centric ("genetic") and metabolite-centric mode ("metab") which allows users to identify enriched pathways driven by significant genes or metabolites, respectively.