Man pages for CePa
Centrality-Based Pathway Enrichment

cepaApply CePa algorithm on a single pathway
cepa.allApply CePa algorithm on a list of pathways under multiple...
cepa.all.paralleluse CePa package through parallel computing
cepa.oraApply centrality-extended ORA on a single pathway
cepa.ora.allApply centrality-extented ORA on a list of pathways
CePa-packageCentrality-based pathway enrichment
cepa.univariateApply centrality-extended GSA on a single pathway
cepa.univariate.allApply centrality-extented GSA on a list of pathways
gene.listDifferential gene list and background gene list
generate.pathwayGenerate igraph object from edge list
get.cepaget single cepa object from cepa.all object
pathway.nodesnames of the pathway nodes
PID.dbpathway catalogues from Pathway Interaction Database(PID)
plot.cepaPlot the cepa object
plot.cepa.allplot the cepa.all object
plotGraphPlot graph for the pathway network
plotNullPlot the null distribution of the pathway score
plot.pathway.catalogueplot pathway.catalogue object
print.cepaprint the cepa object
print.cepa.allprint the cepa.all object
print.pathway.catalogueprint pathway.catalogue object
p.tableTable of p-values of pathways
radialityCalculate radiality centrality
reachCalculate largest reach centrality
read.clsRead CLS file which stores the phenotype data
read.gctRead GCT format file which stores the expression values
reportGenerate report for CePa analysis
sampleLabelGenerate data structure of sample labels
set.pathway.cataloguestore pathway data and pre-processing
spreadCalculate radiality centrality
CePa documentation built on June 5, 2018, 1:03 a.m.