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PCpheno (version 1.32.0)

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

1.32.0

License

Artistic-2.0

Maintainer

Nolwenn Le Meur

Last Published

February 15th, 2017

Functions in PCpheno (1.32.0)

categoryToEntrezBuilder

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

Class "CoHyperGParams"
overlap

Count the number of proteins shared by protein complexes
OsterbergRaw

Data from Osterberg at al. 2006
HI

Data from Deutshbauer et al. (2005)
KEGG2SCISI

Mapping between KEGG and ScISI
gtResult-class

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

Data from Lesage et al. 2005
GiaeverPheno

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

Graph theory to test associations between two or more relationships
KastenmayerRaw

Data from Kastenmayer et al. 2006
PCpheno-package

Linkage between Protein Complexes, Pathways, and Phenotypes
truncName

Truncate character strings
testResult-class

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

Saccharomyces Genome Database list of phenotypic data
reduceM

Resize a matrix
YEASTOHNOLOG

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

Observed versus Expected Ratios
complexStatus

Complex Status
plot

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

Test the association between AP-MS data and phenotype
getDescr

Get formatted annotation data
DudleyPheno

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

Get fitness defect genes
buildFDMat

Build fitness defect contingency matrix
CoHyperGResult-class

Class "CoHyperGResult"
deResult-class

A class for representing the result of a densityEstimate test.