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 |