# Centrality-Based Pathway Enrichment

## Documentation for package ‘CePa’ version 0.8.0

- 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