PCpheno: Phenotypes and cellular organizational units

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

AuthorNolwenn Le Meur and Robert Gentleman
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...

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

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

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