Centrality-Based Pathway Enrichment


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Documentation for package ‘CePa’ version 0.7.0

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CePa-package Centrality-based pathway enrichment
cepa Apply CePa algorithm on a single pathway
cepa.all Apply CePa algorithm on a list of pathways under multiple centralities
cepa.all.parallel use CePa package through parallel computing
cepa.ora Apply centrality-extended ORA on a single pathway
cepa.ora.all Apply centrality-extented ORA on a list of pathways
cepa.univariate Apply centrality-extended GSA on a single pathway
cepa.univariate.all Apply centrality-extented GSA on a list of pathways
gene.list Differential gene list and background gene list
generate.pathway Generate igraph object from edge list
get.cepa get single cepa object from cepa.all object
p.table Table of p-values of pathways
pathway.nodes names of the pathway nodes
PID.db pathway catalogues from Pathway Interaction Database(PID)
plot.cepa Plot the cepa object
plot.cepa.all plot the cepa.all object
plot.pathway.catalogue plot pathway.catalogue object
plotGraph Plot graph for the pathway network
plotNull Plot the null distribution of the pathway score
print.cepa print the cepa object
print.cepa.all print the cepa.all object
print.pathway.catalogue print pathway.catalogue object
radiality Calculate radiality centrality
reach Calculate largest reach centrality
read.cls Read CLS file which stores the phenotype data
read.gct Read GCT format file which stores the expression values
report Generate report for CePa analysis
sampleLabel Generate data structure of sample labels
set.pathway.catalogue store pathway data and pre-processing
spread Calculate radiality centrality