UpdateIntegPathwayAnalysis: Update integrative pathway analysis for new input list

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

Update integrative pathway analysis for new input list

Description

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

Usage

UpdateIntegPathwayAnalysis(mSetObj=NA, qids, file.nm, 
topo="dc", enrich="hyper", libOpt="integ")

Arguments

mSetObj	Input name of the created mSet Object
qids	Input the query IDs
file.nm	Input the name of the file
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.

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MetaboAnalystR documentation built on Dec. 23, 2024, 3:44 p.m.