Man pages for martahidalgo/hipathia
HiPathia

annotate.pathsAnnotates functions to pathways
create.reportCreate visualization HTML
do.pcaPerforms a Principal Components Analysis
do.wilcoxonApply Wilcoxon test
get.highest.sig.ancestorGet highest common GO ancestor of GO annotations
get.path.namesTranlates path IDs to path names
get.paths.matrixGets the matrix of subpathway activation values
get.pathway.functionsReturns functions related to a pathway
get.pathways.annotationsGet Pathways functional annotations
get.pathways.listLists the IDs of the pathways in a pathways object
get.pathways.summaryCompute pathway summary
heatmap.plotPlots subpathways heatmap
hheadHead function for matrices
hipathiaComputes the level of activation of the subpathways for each...
igraphs.upgradeUpgrade igraphs to current version
is.acceptedChecks whether a species is accepted
load.annofunsLoads annotations object
load.annotsLoads functional annotations
load.entrez.hgncLoads table of translation from HGNC to Entrez
load.gobpLoads GO Annotations
load.gobp.frameLoads GO graph information
load.gobp.netLoads GO graph
load.mgiLoads object with graph information
load.pathwaysLoads the pathways object.
load.pseudo.mgiLoads object with pseudo graph information
load.unibpLoads Uniprot annotations
load.xrefLoads table of references
multiple.pca.plotPlots multiple components of a PCA
node.color.per.deColors of the nodes by its differential expression
normalize.dataNormalize expression data to be used in 'hipathia'
normalize.pathsNormalize the pathway matrix by rows
paths.to.go.ancestorCreate path results table with highest significant GO...
pathway.comparison.plotPlots pathway with colored significant paths
pca.plotPlots two components of a PCA
quantify.termsComputes the level of activation of the functions related to...
save.resultsSave results to folder
translate.matrixTranslation of the rownames IDs to Entrez IDs.
visualize.reportVisualize a HiPathia report
martahidalgo/hipathia documentation built on Jan. 15, 2018, 12:54 a.m.