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" |
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<-,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" |
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<-,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<-,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) |