Entry: CoHyperGParams-class
Aliases: CoHyperGParams-class conditional conditional<- geneIds<- isConditional ontology ontology<- pvalueCutoff<- testDirection<- universeGeneIds HyperGParams-class geneIds,HyperGParams-method geneIds<-,HyperGParams,logical-method geneIds<-,HyperGParams-method annotation,HyperGParams-method conditional,HyperGParams-method ontology,HyperGParams-method pvalueCutoff,HyperGParams-method pvalueCutoff<-,HyperGParams-method testDirection,HyperGParams-method testDirection<-,HyperGParams-method universeGeneIds,HyperGParams-method universeBuilder,CoHyperGParams-method hyperGTest,CoHyperGParams-method isConditional,HyperGParams-method categoryName categoryName,HyperGParams-method
Keywords: classes
Description: Class "CoHyperGParams"
URL: ../../../library/PCpheno/html/CoHyperGParams-class.html

Entry: CoHyperGResult-class
Aliases: CoHyperGResult-class summary,CoHyperGResult-method geneCounts,CoHyperGResult-method pvalues,CoHyperGResult-method oddsRatios,CoHyperGResult-method universeCounts,CoHyperGResult-method expectedCounts,CoHyperGResult-method
Keywords: classes
Description: Class "CoHyperGResult"
URL: ../../../library/PCpheno/html/CoHyperGResult-class.html

Entry: DudleyPheno
Aliases: Dudley DudleyGenelist DudleyPhenoFull DudleyPhenoM Dudleyresult DudleySign
Keywords: datasets
Description: List of fitness defect score generated from Dudley et al 2005
URL: ../../../library/PCpheno/html/Dudley.html

Entry: GiaeverPheno
Aliases: GiaeverPheno GiaeverGene GiaeverExpCdt Giaeverresult
Keywords: datasets
Description: List of fitness defect score generated from Giaever et al 2002
URL: ../../../library/PCpheno/html/Giaever.html

Entry: HI
Aliases: HI
Keywords: datasets
Description: Data from Deutshbauer et al. (2005)
URL: ../../../library/PCpheno/html/HI.html

Entry: KEGG2SCISI
Aliases: KEGG2SCISI
Keywords: data manip
Description: Mapping between KEGG and ScISI
URL: ../../../library/PCpheno/html/KEGG2SCISI.html

Entry: KastenmayerRaw
Aliases: KastenmayerRaw
Keywords: datasets
Description: Data from Kastenmayer et al. 2006
URL: ../../../library/PCpheno/html/Kastenmayer.html

Entry: LesageRaw
Aliases: LesageRaw
Keywords: datasets
Description: Data from Lesage et al. 2005
URL: ../../../library/PCpheno/html/Lesage.html

Entry: OsterbergRaw
Aliases: OsterbergRaw
Keywords: datasets
Description: Data from Osterberg at al. 2006
URL: ../../../library/PCpheno/html/Osterberg.html

Entry: PCpheno-package
Aliases: PCpheno-package PCpheno
Keywords: package
Description: Linkage between Protein Complexes, Pathways, and Phenotypes
URL: ../../../library/PCpheno/html/PCpheno.package.html

Entry: SGDphenoL
Aliases: SGDphenoL
Keywords: datasets
Description: Saccharomyces Genome Database list of phenotypic data
URL: ../../../library/PCpheno/html/SGDphenoL.html

Entry: YEASTOHNOLOG
Aliases: YEASTOHNOLOG
Keywords: datasets
Description: List of ohnolog gene pairs from Byrne, K.P and Wolfe, K.H (2005)
URL: ../../../library/PCpheno/html/YEASTOHNOLOG.html

Entry: buildFDMat
Aliases: buildFDMat
Keywords: data manip
Description: Build fitness defect contingency matrix
URL: ../../../library/PCpheno/html/buildFDMat.html

Entry: categoryToEntrezBuilder
Aliases: categoryToEntrezBuilder categoryToEntrezBuilder,CoHyperGParams-method
Keywords: manip
Description: Return a list mapping multi-protein complexes IDs to YEAST ids
URL: ../../../library/PCpheno/html/categoryToEntrezBuilder.html

Entry: complexStatus
Aliases: complexStatus
Keywords: data manip
Description: Complex Status
URL: ../../../library/PCpheno/html/complexStatus.html

Entry: deResult-class
Aliases: deResult-class
Keywords: classes
Description: A class for representing the result of a densityEstimate test.
URL: ../../../library/PCpheno/html/deResult-class.html

Entry: densityEstimate
Aliases: densityEstimate
Keywords: data manip
Description: Observed versus Expected Ratios
URL: ../../../library/PCpheno/html/densityEstimate.html

Entry: getDescr
Aliases: getDescr
Keywords: manip
Description: Get formatted annotation data
URL: ../../../library/PCpheno/html/getDescr.html

Entry: getFDgene
Aliases: getFDgene
Keywords: data manip
Description: Get fitness defect genes
URL: ../../../library/PCpheno/html/getFDgene.html

Entry: graphTheory
Aliases: graphTheory
Keywords: data manip
Description: Graph theory to test associations between two or more relationships
URL: ../../../library/PCpheno/html/graphTheory.html

Entry: gtResult-class
Aliases: gtResult-class
Keywords: classes
Description: A class for representing the result of a graphTheory test.
URL: ../../../library/PCpheno/html/gtResult-class.html

Entry: overlap
Aliases: overlap
Keywords: data manip
Description: Count the number of proteins shared by protein complexes
URL: ../../../library/PCpheno/html/overlap.html

Entry: plot
Aliases: plot plot,deResult-method plot,gtResult-method plot,deResult,missing-method plot,gtResult,missing-method
Keywords: data manip
Description: Graphical method to represent the result of the density or graph test.
URL: ../../../library/PCpheno/html/plot.html

Entry: ppiInteract
Aliases: ppiInteract
Keywords: data manip
Description: Test the association between AP-MS data and phenotype
URL: ../../../library/PCpheno/html/ppiInteraction.html

Entry: reduceM
Aliases: reduceM
Keywords: data manip
Description: Resize a matrix
URL: ../../../library/PCpheno/html/reduceM.html

Entry: testResult-class
Aliases: testResult-class
Keywords: classes
Description: A virtual class for representing the result of a test.
URL: ../../../library/PCpheno/html/testResult-class.html

Entry: truncName
Aliases: truncName
Keywords: data manip
Description: Truncate character strings
URL: ../../../library/PCpheno/html/truncName.html
