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PCpheno (version 1.28.0)

Phenotypes and cellular organizational units

Description

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

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Version

Version

1.28.0

License

Artistic-2.0

Maintainer

Nolwenn Le Meur

Last Published

February 15th, 2017

Functions in PCpheno (1.28.0)

complexStatus

Complex Status
categoryToEntrezBuilder

Return a list mapping multi-protein complexes IDs to YEAST ids
deResult-class

A class for representing the result of a densityEstimate test.
DudleyPheno

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

Build fitness defect contingency matrix
getDescr

Get formatted annotation data
getFDgene

Get fitness defect genes
CoHyperGParams-class

Class "CoHyperGParams"
CoHyperGResult-class

Class "CoHyperGResult"
densityEstimate

Observed versus Expected Ratios
KastenmayerRaw

Data from Kastenmayer et al. 2006
GiaeverPheno

List of fitness defect score generated from Giaever et al 2002
PCpheno-package

Linkage between Protein Complexes, Pathways, and Phenotypes
graphTheory

Graph theory to test associations between two or more relationships
overlap

Count the number of proteins shared by protein complexes
KEGG2SCISI

Mapping between KEGG and ScISI
LesageRaw

Data from Lesage et al. 2005
OsterbergRaw

Data from Osterberg at al. 2006
gtResult-class

A class for representing the result of a graphTheory test.
HI

Data from Deutshbauer et al. (2005)
YEASTOHNOLOG

List of ohnolog gene pairs from Byrne, K.P and Wolfe, K.H (2005)
plot

Graphical method to represent the result of the density or graph test.
SGDphenoL

Saccharomyces Genome Database list of phenotypic data
ppiInteract

Test the association between AP-MS data and phenotype
testResult-class

A virtual class for representing the result of a test.
reduceM

Resize a matrix
truncName

Truncate character strings