Tools for manipulating GO and microarrays.


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Documentation for package `GOstats' version 2.0.4

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GOstats-package Tools for manipulating GO and microarrays.
Bdists Distance matrices for the BCR/ABL and NEG subgroups.
combGOGraph Defunct Functions in GOstats Package
compCorrGraph A function to compute a correlation based graph from Gene Expression Data
compGdist A function to compute the distance between pairs of nodes in a graph.
condGeneIdUniverse Class "GOHyperGResult"
condGeneIdUniverse,GOHyperGResult-method Class "GOHyperGResult"
description,GOHyperGResult-method Class "GOHyperGResult"
enumPairs Triad Functions
expectedCounts Class "GOHyperGResult"
expectedCounts,GOHyperGResult-method Class "GOHyperGResult"
geneCounts,GOHyperGResult-method Class "GOHyperGResult"
geneIdUniverse Class "GOHyperGResult"
geneIdUniverse,GOHyperGResult-method Class "GOHyperGResult"
getGoGraph Construct the GO graph given a set of leaves.
getGoGraph,GOHyperGParams,character-method Construct the GO graph given a set of leaves.
goDag Class "GOHyperGResult"
goDag,GOHyperGResult-method Class "GOHyperGResult"
GOGraph Construct the GO graph given a set of leaves.
GOHyperG Hypergeometric Tests for GO
GOHyperGResult-class Class "GOHyperGResult"
GOLeaves Identify the leaves in a GO Graph
GOstats Tools for manipulating GO and microarrays.
GOstats-defunct Defunct Functions in GOstats Package
htmlReport,GOHyperGResult-method Class "GOHyperGResult"
hyperG2Affy A List of Affymetrix IDs from GOIDs
hyperGtable Table from GOHyperG
hyperGTest Hypergeometric Tests for GO term association
hyperGTest,GOHyperGParams-method Hypergeometric Tests for GO term association
idx2dimnames Index to Dimnames
isConditional,GOHyperGResult-method Class "GOHyperGResult"
isTriad Triad Functions
makeGOGraph Construct a GO Graph
Ndists Distance matrices for the BCR/ABL and NEG subgroups.
notConn Find genes that are not connected to the others.
oddsRatios Class "GOHyperGResult"
oddsRatios,GOHyperGResult-method Class "GOHyperGResult"
oneGOGraph Construct the GO graph given a set of leaves.
probeSetSummary Summarize Probe Sets Associated with a hyperGTest Result
pvalues,GOHyperGResult-method Class "GOHyperGResult"
reduce2Degreek Triad Functions
shortestPath Shortest Path Analysis
simLL Functions to compute similarities between GO graphs and also between LocusLink IDs based on their induced GO graphs.
simLP Functions to compute similarities between GO graphs and also between LocusLink IDs based on their induced GO graphs.
simUI Functions to compute similarities between GO graphs and also between LocusLink IDs based on their induced GO graphs.
summary,GOHyperGResult-method Class "GOHyperGResult"
triad Triad Functions
triadCensus Triad Functions
universeCounts,GOHyperGResult-method Class "GOHyperGResult"
universeMappedCount,GOHyperGResult-method Class "GOHyperGResult"