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) |