# Tools for manipulating GO and microarrays.

## Documentation for package ‘GOstats’ version 2.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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,GOHyperGResult-method | Class "GOHyperGResult"
conditional,GOHyperGResult-method | Class "GOHyperGResult"
enumPairs | Triad Functions
expectedCounts,GOHyperGResult-method | Class "GOHyperGResult"
geneCounts,GOHyperGResult-method | 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 | (DEPRECATED) Hypergeometric Tests for GO
GOHyperGResult-class | Class "GOHyperGResult"
GOLeaves | DEPRECATED 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 | Defunct Functions in GOstats Package
hyperGtable | Defunct Functions in GOstats Package
hyperGTest | Hypergeometric Tests for GO term association
hyperGTest,GOHyperGParams-method | Hypergeometric Tests for GO term association
idx2dimnames | Index to Dimnames
inducedTermGraph | Extraction and Plotting of GO Terms from a GOHyperGResult Object
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,GOHyperGResult-method | Class "GOHyperGResult"
oneGOGraph | Construct the GO graph given a set of leaves.
plotGOTermGraph | Extraction and Plotting of GO Terms from a GOHyperGResult Object
probeSetSummary | Summarize Probe Sets Associated with a hyperGTest Result
pvalues,GOHyperGResult-method | Class "GOHyperGResult"
reduce2Degreek | Triad Functions
selectedGenes | Class "GOHyperGResult"
shortestPath | Shortest Path Analysis
simLL | Functions to compute similarities between GO graphs and also between Entrez Gene IDs based on their induced GO graphs.
simLP | Functions to compute similarities between GO graphs and also between Entrez Gene IDs based on their induced GO graphs.
simUI | Functions to compute similarities between GO graphs and also between Entrez Gene IDs based on their induced GO graphs.
summary,GOHyperGResult-method | Class "GOHyperGResult"
termGraphs | Extraction and Plotting of GO Terms from a GOHyperGResult Object
triad | Triad Functions
triadCensus | Triad Functions