# Phenotypes and cellular organizational units

## Documentation for package ‘PCpheno’ version 1.6.0

## User Guides and Package Vignettes

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## Help Pages

PCpheno-package | Linkage between Protein Complexes, Pathways, and Phenotypes
annotation,HyperGParams-method | Class "CoHyperGParams"
buildFDMat | Build fitness defect contingency matrix
categoryName | Class "CoHyperGParams"
categoryName,HyperGParams-method | Class "CoHyperGParams"
categoryToEntrezBuilder | Return a list mapping multi-protein complexes IDs to YEAST ids
categoryToEntrezBuilder,CoHyperGParams-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,HyperGParams-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,CoHyperGResult-method | Class "CoHyperGResult"
geneCounts,CoHyperGResult-method | Class "CoHyperGResult"
geneIds,HyperGParams-method | Class "CoHyperGParams"
geneIds<- | Class "CoHyperGParams"
geneIds<-,HyperGParams,logical-method | Class "CoHyperGParams"
geneIds<-,HyperGParams-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,CoHyperGParams-method | Class "CoHyperGParams"
isConditional | Class "CoHyperGParams"
isConditional,HyperGParams-method | Class "CoHyperGParams"
KastenmayerRaw | Data from Kastenmayer et al. 2006
KEGG2SCISI | Mapping between KEGG and ScISI
LesageRaw | Data from Lesage et al. 2005
oddsRatios,CoHyperGResult-method | Class "CoHyperGResult"
ontology | Class "CoHyperGParams"
ontology,HyperGParams-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,deResult,missing-method | Graphical method to represent the result of the density or graph test.
plot,deResult-method | Graphical method to represent the result of the density or graph test.
plot,gtResult,missing-method | Graphical method to represent the result of the density or graph test.
plot,gtResult-method | Graphical method to represent the result of the density or graph test.
ppiInteract | Test the association between AP-MS data and phenotype
pvalueCutoff,HyperGParams-method | Class "CoHyperGParams"
pvalueCutoff<- | Class "CoHyperGParams"
pvalueCutoff<-,HyperGParams-method | Class "CoHyperGParams"
pvalues,CoHyperGResult-method | Class "CoHyperGResult"
reduceM | Resize a matrix
SGDphenoL | Saccharomyces Genome Database list of phenotypic data
summary,CoHyperGResult-method | Class "CoHyperGResult"
testDirection,HyperGParams-method | Class "CoHyperGParams"
testDirection<- | Class "CoHyperGParams"
testDirection<-,HyperGParams-method | Class "CoHyperGParams"
testResult-class | A virtual class for representing the result of a test.
truncName | Truncate character strings
universeBuilder,CoHyperGParams-method | Class "CoHyperGParams"
universeCounts,CoHyperGResult-method | Class "CoHyperGResult"
universeGeneIds | Class "CoHyperGParams"
universeGeneIds,HyperGParams-method | Class "CoHyperGParams"
YEASTOHNOLOG | List of ohnolog gene pairs from Byrne, K.P and Wolfe, K.H (2005)