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CePa (version 0.8.1)

Centrality-Based Pathway Enrichment

Description

It aims to find significant pathways through network topology information. It has several advantages compared with current pathway enrichment tools. First, pathway node instead of single gene is taken as the basic unit when analysing networks to meet the fact that genes must be constructed into complexes to hold normal functions. Second, multiple network centrality measures are applied simultaneously to measure importance of nodes from different aspects to make a full view on the biological system. CePa extends standard pathway enrichment methods, which include both over-representation analysis procedure and gene-set analysis procedure. .

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Install

install.packages('CePa')

Monthly Downloads

574

Version

0.8.1

License

GPL (>= 2)

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Maintainer

Last Published

October 8th, 2024

Functions in CePa (0.8.1)

plot.cepa.all

plot the cepa.all object
read.gct

Read GCT format file which stores the expression values
read.cls

Read CLS file which stores the phenotype data
print.cepa.all

print the cepa.all object
set.pathway.catalogue

store pathway data and pre-processing
spread

Calculate radiality centrality
print.pathway.catalogue

print pathway.catalogue object
radiality

Calculate radiality centrality
reach

Calculate largest reach centrality
sampleLabel

Generate data structure of sample labels
report

Generate report for CePa analysis
CePa-package

Centrality-based pathway enrichment
cepa.all

Apply CePa algorithm on a list of pathways under multiple centralities
cepa.univariate

Apply centrality-extended GSA on a single pathway
cepa.ora

Apply centrality-extended ORA on a single pathway
print.cepa

print the cepa object
plot.cepa

Plot the cepa object
plotGraph

Plot graph for the pathway network
plot.pathway.catalogue

plot pathway.catalogue object
generate.pathway

Generate igraph object from edge list
p.table

Table of p-values of pathways
cepa

Apply CePa algorithm on a single pathway
cepa.univariate.all

Apply centrality-extented GSA on a list of pathways
pathway.nodes

names of the pathway nodes
cepa.all.parallel

use CePa package through parallel computing
gene.list

Differential gene list and background gene list
cepa.ora.all

Apply centrality-extented ORA on a list of pathways
PID.db

pathway catalogues from Pathway Interaction Database(PID)
plotNull

Plot the null distribution of the pathway score
get.cepa

get single cepa object from cepa.all object