Phenotypes and cellular organizational units


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Documentation for package ‘PCpheno’ version 1.40.0

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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)