R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 19 found.
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CoHyperGParams-class (Package: PCpheno) : Class "CoHyperGParams"

A parameter class for representing all parameters needed for running the hyperGTest method with multiprotein complexes.

● Data Source: BioConductor
● Keywords: classes
● Alias: CoHyperGParams-class, HyperGParams-class, annotation,HyperGParams-method, categoryName, categoryName,HyperGParams-method, conditional, conditional,HyperGParams-method, conditional<-, geneIds,HyperGParams-method, geneIds<-, geneIds<-,HyperGParams,logical-method, geneIds<-,HyperGParams-method, hyperGTest,CoHyperGParams-method, isConditional, isConditional,HyperGParams-method, ontology, ontology,HyperGParams-method, ontology<-, pvalueCutoff,HyperGParams-method, pvalueCutoff<-, pvalueCutoff<-,HyperGParams-method, testDirection,HyperGParams-method, testDirection<-, testDirection<-,HyperGParams-method, universeBuilder,CoHyperGParams-method, universeGeneIds, universeGeneIds,HyperGParams-method
● 0 images

CoHyperGResult-class (Package: PCpheno) : Class "CoHyperGResult"

This class represents the results of a test for over-representation of genes in a selected gene set based among protein complexes upon the Hypergeometric distribution.

● Data Source: BioConductor
● Keywords: classes
● Alias: CoHyperGResult-class, expectedCounts,CoHyperGResult-method, geneCounts,CoHyperGResult-method, oddsRatios,CoHyperGResult-method, pvalues,CoHyperGResult-method, summary,CoHyperGResult-method, universeCounts,CoHyperGResult-method
● 0 images

KEGG2SCISI (Package: PCpheno) : Mapping between KEGG and ScISI

Count the number of genes shared between a KEGG pathway and a protein complex from the ScISI interactome.

● Data Source: BioConductor
● Keywords: data, manip
● Alias: KEGG2SCISI
● 0 images

PCpheno-package (Package: PCpheno) :

Tools to integrate, annotate and search for associations between phenotypes, protein complexes, and pathways.

● Data Source: BioConductor
● Keywords: package
● Alias: PCpheno, PCpheno-package
● 0 images

buildFDMat (Package: PCpheno) : Build fitness defect contingency matrix

Function to build a fitness defect contingency matrix where rows correspond to tested genes and columns to experimental conditions.

● Data Source: BioConductor
● Keywords: data, manip
● Alias: buildFDMat
● 0 images

categoryToEntrezBuilder (Package: PCpheno) : Return a list mapping multi-protein complexes IDs to YEAST ids

Return a list mapping multi-protein complexes (category) IDs to the YEAST ids annotated at the category id.

● Data Source: BioConductor
● Keywords: manip
● Alias: categoryToEntrezBuilder, categoryToEntrezBuilder,CoHyperGParams-method
● 0 images

complexStatus (Package: PCpheno) : Complex Status

Categorize the complex whether or not a complex is composed of a significant number of genes involved in a particular phenotype than expected by chance.

● Data Source: BioConductor
● Keywords: data, manip
● Alias: complexStatus
● 0 images

deResult-class (Package: PCpheno) : A class for representing the result of a densityEstimate test.

A class for representing the result of a densityEstimate test.

● Data Source: BioConductor
● Keywords: classes
● Alias: deResult-class
● 1 images

densityEstimate (Package: PCpheno) : Observed versus Expected Ratios

Function to calculate the ratio of genes that characterize a phenotype (observed) among the genes that characterize a biological complex versus the ratio of a set of randomly sampled genes (expected) among the genes that characterize a biological complex.

● Data Source: BioConductor
● Keywords: data, manip
● Alias: densityEstimate
● 0 images

getDescr (Package: PCpheno) : Get formatted annotation data

Function to retrieve the annotation of multi-protein complexes or pathways via GO, MIPS or KEGG.

● Data Source: BioConductor
● Keywords: manip
● Alias: getDescr
● 0 images