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PCpheno (version 1.34.0)

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

1.34.0

License

Artistic-2.0

Maintainer

Nolwenn Le Meur

Last Published

February 15th, 2017

Functions in PCpheno (1.34.0)

testResult-class

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

List of fitness defect score generated from Giaever et al 2002
complexStatus

Complex Status
KEGG2SCISI

Mapping between KEGG and ScISI
HI

Data from Deutshbauer et al. (2005)
gtResult-class

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

Build fitness defect contingency matrix
SGDphenoL

Saccharomyces Genome Database list of phenotypic data
LesageRaw

Data from Lesage et al. 2005
truncName

Truncate character strings
overlap

Count the number of proteins shared by protein complexes
categoryToEntrezBuilder

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

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

Class "CoHyperGParams"
deResult-class

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

Observed versus Expected Ratios
PCpheno-package

Linkage between Protein Complexes, Pathways, and Phenotypes
CoHyperGResult-class

Class "CoHyperGResult"
getFDgene

Get fitness defect genes
plot

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

Get formatted annotation data
KastenmayerRaw

Data from Kastenmayer et al. 2006
OsterbergRaw

Data from Osterberg at al. 2006
YEASTOHNOLOG

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

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

Graph theory to test associations between two or more relationships
reduceM

Resize a matrix