Centrality-Based Pathway Enrichment

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Documentation for package ‘CePa’ version 0.8.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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