Clustering Enrichment Analysis


[Up] [Top]

Documentation for package ‘CLEAN’ version 1.2.7

Help Pages

CLEAN-package Clustering Enrichment Analysis
atr2r Functions to import files in TreeView format into R.
bCa Sets of p-values derived from two breast cancer data sets.
call.treeview Function to call the standalone fTreeView Java application
cdt2r Functions to import files in TreeView format into R.
CLEAN Clustering Enrichment Analysis
cMap A set of p-values derived from the Connectivity Map dataset.
convertFunctionalCategories Function to convert Entrez gene ID-based functional categories from one
convertGeneTable Function to convert Entrez gene ID-based functional categories from one
funcClustAnnot Wrapper function to perform functional Clustering Enrichment Analysis
geneListEnrichment Wrapper function to perform functional Clustering Enrichment Analysis
generateTreeViewFiles Wrapper function to perform functional Clustering Enrichment Analysis
geneSigInClustering Auxiliary functions to funcClustAnnot and geneListEnrichment
geneSigInClustering_nullDistr Auxiliary functions to funcClustAnnot and geneListEnrichment
geneSigInList Auxiliary functions to funcClustAnnot and geneListEnrichment
genesInEnrichedCategories Function to intersect a gene list with enriched categories
getAllClusters Auxiliary functions to funcClustAnnot and geneListEnrichment
getBinarySubTree Get the left or right subtree of a given hierarchical clustering.
getFunctionalCategories Retrieve functional categories from species-specific library.
gimmOut An gimmR object, i.e. a list containing a dataframe with gene
GRS Function to calculate the Generalized Random Set statistic to perform
gtr2r Functions to import files in TreeView format into R.
initializeCategories Auxiliary functions to funcClustAnnot and geneListEnrichment
insertCdt Auxiliary functions to funcClustAnnot and geneListEnrichment
LRpath Testing GO terms or KEGG with logistic regression
nonHierarchicalClustering Convert a non-hierarchical clustering into hierarchical tree-structure
plotCLEANscore Function to generate a diagnostic plot using the CLEAN score
primSetSigInClustering Auxiliary functions to funcClustAnnot and geneListEnrichment
pruneMinFDR Auxiliary functions to funcClustAnnot and geneListEnrichment
qvalue Estimate the q-values for a given set of p-values
r2atr Functions to generate fTreeView files
r2cdt Functions to generate fTreeView files
r2fni Functions to generate fTreeView files
r2gtr Functions to generate fTreeView files
RandomSet Testing GO terms, KEGG pathways, and other categories with Random Set
RS Testing GO terms, KEGG pathways, and other categories with Random Set
runCLEAN Wrapper function to perform functional Clustering Enrichment Analysis
significantCategories Auxiliary functions to funcClustAnnot and geneListEnrichment