PCpheno: Phenotypes and cellular organizational units

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

Author
Nolwenn Le Meur and Robert Gentleman
Date of publication
None
Maintainer
Nolwenn Le Meur <nlemeur@gmail.com>
License
Artistic-2.0
Version
1.36.0

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...

Files in this package

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