PCpheno: Phenotypes and cellular organizational units
Version 1.38.0

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

AuthorNolwenn Le Meur and Robert Gentleman
Bioconductor views GraphAndNetwork Network Proteomics
Date of publicationNone
MaintainerNolwenn Le Meur <nlemeur@gmail.com>
LicenseArtistic-2.0
Version1.38.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PCpheno")

Popular man pages

buildFDMat: Build fitness defect contingency matrix
deResult-class: A class for representing the result of a densityEstimate...
Dudley: List of fitness defect score generated from Dudley et al 2005
getFDgene: Get fitness defect genes
Osterberg: Data from Osterberg at al. 2006
plot: Graphical method to represent the result of the density or...
YEASTOHNOLOG: List of ohnolog gene pairs from Byrne, K.P and Wolfe, K.H...
See all...

All man pages Function index File listing

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

CoHyperGParams-class Man page
CoHyperGResult-class Man page
Dudley Man page
DudleyGenelist Man page
DudleyPhenoFull Man page
DudleyPhenoM Man page
DudleySign Man page
Dudleyresult Man page
GiaeverExpCdt Man page
GiaeverGene Man page
GiaeverPheno Man page
Giaeverresult Man page
HI Man page
HyperGParams-class Man page
KEGG2SCISI Man page Source code
KastenmayerRaw Man page
LesageRaw Man page
OsterbergRaw Man page
PCpheno Man page
PCpheno-package Man page
SGDphenoL Man page
YEASTOHNOLOG Man page
annotatePC Source code
annotation,HyperGParams-method Man page
buildFDMat Man page Source code
categoryName Man page
categoryName,HyperGParams-method Man page
categoryToEntrezBuilder Man page
categoryToEntrezBuilder,CoHyperGParams-method Man page
complexStatus Man page Source code
conditional Man page
conditional,HyperGParams-method Man page
conditional<- Man page
deResult-class Man page
densityEstimate Man page Source code
expectedCounts,CoHyperGResult-method Man page
geneCounts,CoHyperGResult-method Man page
geneIds,HyperGParams-method Man page
geneIds<- Man page
geneIds<-,HyperGParams,logical-method Man page
geneIds<-,HyperGParams-method Man page
getCompToEntrezMap Source code
getDescr Man page Source code
getFDgene Man page Source code
graphTheory Man page Source code
gtResult-class Man page
hyperGTest,CoHyperGParams-method Man page
isConditional Man page
isConditional,HyperGParams-method Man page
list2matrix Source code
logistPheno Source code
oddsRatios,CoHyperGResult-method Man page
ontology Man page
ontology,HyperGParams-method Man page
ontology<- Man page
overlap Man page Source code
plot Man page
plot,deResult,missing-method Man page
plot,deResult-method Man page
plot,gtResult,missing-method Man page
plot,gtResult-method Man page
ppiInteract Man page Source code
pvalueCutoff,HyperGParams-method Man page
pvalueCutoff<- Man page
pvalueCutoff<-,HyperGParams-method Man page
pvalues,CoHyperGResult-method Man page
reduceM Man page Source code
summary,CoHyperGResult-method Man page
summaryMap Source code
testDirection,HyperGParams-method Man page
testDirection<- Man page
testDirection<-,HyperGParams-method Man page
testResult-class Man page
truncName Man page Source code
universeBuilder,CoHyperGParams-method Man page
universeCounts,CoHyperGResult-method Man page
universeGeneIds Man page
universeGeneIds,HyperGParams-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/KEGG2SCISI.R
R/OU-methods.R
R/annotation-functions.R
R/categoryToEntrezBuilder-methods.R
R/complexStatus.R
R/giaever-functions.R
R/hyperGResults-accessors.R
R/hyperGtest-methods.R
R/logistPheno.R
R/omnibusTest-functions.R
R/omnibusTest-methods.R
R/ppiInteract.R
R/utils.R
build
build/vignette.rds
data
data/DudleyGenelist.rda
data/DudleyPhenoFull.rda
data/DudleyPhenoM.rda
data/DudleySign.rda
data/Dudleyresult.rda
data/GiaeverExpCdt.rda
data/GiaeverGene.rda
data/GiaeverPheno.rda
data/Giaeverresult.rda
data/HI.rda
data/KastenmayerRaw.rda
data/LesageRaw.rda
data/OsterbergRaw.rda
data/SGDphenoL.rda
data/YEASTOHNOLOG.rda
inst
inst/doc
inst/doc/PCpheno.R
inst/doc/PCpheno.Rnw
inst/doc/PCpheno.pdf
man
man/CoHyperGParams-class.Rd
man/CoHyperGResult-class.Rd
man/Dudley.Rd
man/Giaever.Rd
man/HI.Rd
man/KEGG2SCISI.Rd
man/Kastenmayer.Rd
man/Lesage.Rd
man/Osterberg.Rd
man/PCpheno.package.Rd
man/SGDphenoL.Rd
man/YEASTOHNOLOG.Rd
man/buildFDMat.Rd
man/categoryToEntrezBuilder.Rd
man/complexStatus.Rd
man/deResult-class.Rd
man/densityEstimate.Rd
man/getDescr.Rd
man/getFDgene.Rd
man/graphTheory.Rd
man/gtResult-class.Rd
man/overlap.Rd
man/plot.Rd
man/ppiInteraction.Rd
man/reduceM.Rd
man/testResult-class.Rd
man/truncName.Rd
vignettes
vignettes/PCpheno.Rnw
vignettes/reference.bib
PCpheno documentation built on May 20, 2017, 9:28 p.m.

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

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

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