| PCpheno-package | Linkage between Protein Complexes, Pathways, and Phenotypes |
| annotation-method | Class "CoHyperGParams" |
| buildFDMat | Build fitness defect contingency matrix |
| categoryName | Class "CoHyperGParams" |
| categoryName-method | Class "CoHyperGParams" |
| categoryToEntrezBuilder | Return a list mapping multi-protein complexes IDs to YEAST ids |
| categoryToEntrezBuilder-method | Return a list mapping multi-protein complexes IDs to YEAST ids |
| CoHyperGParams-class | Class "CoHyperGParams" |
| CoHyperGResult-class | Class "CoHyperGResult" |
| complexStatus | Complex Status |
| conditional | Class "CoHyperGParams" |
| conditional-method | Class "CoHyperGParams" |
| conditional<- | Class "CoHyperGParams" |
| densityEstimate | Observed versus Expected Ratios |
| deResult-class | A class for representing the result of a densityEstimate test. |
| Dudley | List of fitness defect score generated from Dudley et al 2005 |
| DudleyGenelist | List of fitness defect score generated from Dudley et al 2005 |
| DudleyPhenoFull | List of fitness defect score generated from Dudley et al 2005 |
| DudleyPhenoM | List of fitness defect score generated from Dudley et al 2005 |
| Dudleyresult | List of fitness defect score generated from Dudley et al 2005 |
| DudleySign | List of fitness defect score generated from Dudley et al 2005 |
| expectedCounts-method | Class "CoHyperGResult" |
| geneCounts-method | Class "CoHyperGResult" |
| geneIds-method | Class "CoHyperGParams" |
| geneIds<- | Class "CoHyperGParams" |
| geneIds<--method | Class "CoHyperGParams" |
| getDescr | Get formatted annotation data |
| getFDgene | Get fitness defect genes |
| GiaeverExpCdt | List of fitness defect score generated from Giaever et al 2002 |
| GiaeverGene | List of fitness defect score generated from Giaever et al 2002 |
| GiaeverPheno | List of fitness defect score generated from Giaever et al 2002 |
| Giaeverresult | List of fitness defect score generated from Giaever et al 2002 |
| graphTheory | Graph theory to test associations between two or more relationships |
| gtResult-class | A class for representing the result of a graphTheory test. |
| HI | Data from Deutshbauer et al. (2005) |
| HyperGParams-class | Class "CoHyperGParams" |
| hyperGTest-method | Class "CoHyperGParams" |
| isConditional | Class "CoHyperGParams" |
| isConditional-method | Class "CoHyperGParams" |
| KastenmayerRaw | Data from Kastenmayer et al. 2006 |
| KEGG2SCISI | Mapping between KEGG and ScISI |
| LesageRaw | Data from Lesage et al. 2005 |
| oddsRatios-method | Class "CoHyperGResult" |
| ontology | Class "CoHyperGParams" |
| ontology-method | Class "CoHyperGParams" |
| ontology<- | Class "CoHyperGParams" |
| OsterbergRaw | Data from Osterberg at al. 2006 |
| overlap | Count the number of proteins shared by protein complexes |
| PCpheno | Linkage between Protein Complexes, Pathways, and Phenotypes |
| plot | Graphical method to represent the result of the density or graph test. |
| plot-method | Graphical method to represent the result of the density or graph test. |
| ppiInteract | Test the association between AP-MS data and phenotype |
| pvalueCutoff-method | Class "CoHyperGParams" |
| pvalueCutoff<- | Class "CoHyperGParams" |
| pvalueCutoff<--method | Class "CoHyperGParams" |
| pvalues-method | Class "CoHyperGResult" |
| reduceM | Resize a matrix |
| SGDphenoL | Saccharomyces Genome Database list of phenotypic data |
| summary-method | Class "CoHyperGResult" |
| testDirection-method | Class "CoHyperGParams" |
| testDirection<- | Class "CoHyperGParams" |
| testDirection<--method | Class "CoHyperGParams" |
| testResult-class | A virtual class for representing the result of a test. |
| truncName | Truncate character strings |
| universeBuilder-method | Class "CoHyperGParams" |
| universeCounts-method | Class "CoHyperGResult" |
| universeGeneIds | Class "CoHyperGParams" |
| universeGeneIds-method | Class "CoHyperGParams" |
| YEASTOHNOLOG | List of ohnolog gene pairs from Byrne, K.P and Wolfe, K.H (2005) |