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PCpheno (version 1.30.0)

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

1.30.0

License

Artistic-2.0

Maintainer

Nolwenn Le Meur

Last Published

February 15th, 2017

Functions in PCpheno (1.30.0)

complexStatus

Complex Status
KEGG2SCISI

Mapping between KEGG and ScISI
getDescr

Get formatted annotation data
getFDgene

Get fitness defect genes
KastenmayerRaw

Data from Kastenmayer et al. 2006
densityEstimate

Observed versus Expected Ratios
overlap

Count the number of proteins shared by protein complexes
PCpheno-package

Linkage between Protein Complexes, Pathways, and Phenotypes
ppiInteract

Test the association between AP-MS data and phenotype
plot

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

List of fitness defect score generated from Dudley et al 2005
deResult-class

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

Data from Lesage et al. 2005
OsterbergRaw

Data from Osterberg at al. 2006
CoHyperGParams-class

Class "CoHyperGParams"
CoHyperGResult-class

Class "CoHyperGResult"
GiaeverPheno

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

Graph theory to test associations between two or more relationships
YEASTOHNOLOG

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

Build fitness defect contingency matrix
categoryToEntrezBuilder

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

Truncate character strings
testResult-class

A virtual class for representing the result of a test.
gtResult-class

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

Data from Deutshbauer et al. (2005)
SGDphenoL

Saccharomyces Genome Database list of phenotypic data
reduceM

Resize a matrix