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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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1.34.0
1.32.0
1.30.0
1.28.0
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Version
1.34.0
License
Artistic-2.0
Maintainer
Nolwenn Le Meur
Last Published
January 1st, 1970
Functions in PCpheno (1.34.0)
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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