PerformIntegPathwayAnalysis: Perform integrative pathway analysis

View source: R/enrich_integ.R

PerformIntegPathwayAnalysisR Documentation

Perform integrative pathway analysis

Description

used for integrative analysis as well as general pathways analysis for meta-analysis results

Usage

PerformIntegPathwayAnalysis(mSetObj, topo="dc", enrich="hyper", 
libOpt="integ", integOpt="query")

Arguments

mSetObj

Input name of the created mSet Object

topo

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.

enrich

Method to perform over-representation analysis (ORA) based on either hypergenometrics analysis ("hyper") or Fisher's exact method ("fisher").

libOpt

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.

integOpt

integOpt,default is "query"

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)


xia-lab/MetaboAnalystR documentation built on Sept. 12, 2024, 2:23 p.m.