PCpheno: Phenotypes and cellular organizational units

Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PCpheno")
AuthorNolwenn Le Meur and Robert Gentleman
Bioconductor views GraphAndNetwork Network Proteomics
Date of publicationNone
MaintainerNolwenn Le Meur <nlemeur@gmail.com>
LicenseArtistic-2.0
Version1.36.0

View on Bioconductor

Man pages

buildFDMat: Build fitness defect contingency matrix

categoryToEntrezBuilder: Return a list mapping multi-protein complexes IDs to YEAST...

CoHyperGParams-class: Class "CoHyperGParams"

CoHyperGResult-class: Class "CoHyperGResult"

complexStatus: Complex Status

densityEstimate: Observed versus Expected Ratios

deResult-class: A class for representing the result of a densityEstimate...

Dudley: List of fitness defect score generated from Dudley et al 2005

getDescr: Get formatted annotation data

getFDgene: Get fitness defect genes

Giaever: List of fitness defect score generated from Giaever et al...

graphTheory: Graph theory to test associations between two or more...

gtResult-class: A class for representing the result of a graphTheory test.

HI: Data from Deutshbauer et al. (2005)

Kastenmayer: Data from Kastenmayer et al. 2006

KEGG2SCISI: Mapping between KEGG and ScISI

Lesage: Data from Lesage et al. 2005

Osterberg: Data from Osterberg at al. 2006

overlap: Count the number of proteins shared by protein complexes

PCpheno.package: Linkage between Protein Complexes, Pathways, and Phenotypes

plot: Graphical method to represent the result of the density or...

ppiInteraction: Test the association between AP-MS data and phenotype

reduceM: Resize a matrix

SGDphenoL: Saccharomyces Genome Database list of phenotypic data

testResult-class: A virtual class for representing the result of a test.

truncName: Truncate character strings

YEASTOHNOLOG: List of ohnolog gene pairs from Byrne, K.P and Wolfe, K.H...

Functions

annotation,HyperGParams-method Man page
buildFDMat Man page
categoryName Man page
categoryName,HyperGParams-method Man page
categoryToEntrezBuilder Man page
categoryToEntrezBuilder,CoHyperGParams-method Man page
CoHyperGParams-class Man page
CoHyperGResult-class Man page
complexStatus Man page
conditional Man page
conditional<- Man page
conditional,HyperGParams-method Man page
densityEstimate Man page
deResult-class Man page
Dudley Man page
DudleyGenelist Man page
DudleyPhenoFull Man page
DudleyPhenoM Man page
Dudleyresult Man page
DudleySign Man page
expectedCounts,CoHyperGResult-method Man page
geneCounts,CoHyperGResult-method Man page
geneIds<- Man page
geneIds<-,HyperGParams,logical-method Man page
geneIds<-,HyperGParams-method Man page
geneIds,HyperGParams-method Man page
getDescr Man page
getFDgene Man page
GiaeverExpCdt Man page
GiaeverGene Man page
GiaeverPheno Man page
Giaeverresult Man page
graphTheory Man page
gtResult-class Man page
HI Man page
HyperGParams-class Man page
hyperGTest,CoHyperGParams-method Man page
isConditional Man page
isConditional,HyperGParams-method Man page
KastenmayerRaw Man page
KEGG2SCISI Man page
LesageRaw Man page
oddsRatios,CoHyperGResult-method Man page
ontology Man page
ontology<- Man page
ontology,HyperGParams-method Man page
OsterbergRaw Man page
overlap Man page
PCpheno Man page
PCpheno-package Man page
plot Man page
plot,deResult-method Man page
plot,deResult,missing-method Man page
plot,gtResult-method Man page
plot,gtResult,missing-method Man page
ppiInteract Man page
pvalueCutoff<- Man page
pvalueCutoff<-,HyperGParams-method Man page
pvalueCutoff,HyperGParams-method Man page
pvalues,CoHyperGResult-method Man page
reduceM Man page
SGDphenoL Man page
summary,CoHyperGResult-method Man page
testDirection<- Man page
testDirection<-,HyperGParams-method Man page
testDirection,HyperGParams-method Man page
testResult-class Man page
truncName Man page
universeBuilder,CoHyperGParams-method Man page
universeCounts,CoHyperGResult-method Man page
universeGeneIds Man page
universeGeneIds,HyperGParams-method Man page
YEASTOHNOLOG Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.