CHRListHyperGParams |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
CHRListHyperGParams-class |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
CHRListHyperGResult |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
CHRListHyperGResult-class |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
class:ISAModules |
A set of ISA modules |
coerce,Biclust,ISAModules-method |
Convert ISA modules to a Biclust object, or the opposite |
coerce,ISAModules,Biclust-method |
Convert ISA modules to a Biclust object, or the opposite |
condGeneIdUniverse,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
condGeneIdUniverse,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
condGeneIdUniverse,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
condGeneIdUniverse,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
condGeneIdUniverse,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
condGeneIdUniverse,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
conditional,GOListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
conditional,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
conditional<-,GOListHyperGParams,logical-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
condPlot |
Plot sample scores of a transcription module |
dim,ISAModules-method |
A set of ISA modules |
drive |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive,CHRListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive,GeneralListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive,GOListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive,KEGGListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive,ListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive,miRNAListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive<- |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive<-,CHRListHyperGParams,logical-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive<-,GeneralListHyperGParams,logical-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive<-,GOListHyperGParams,logical-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive<-,KEGGListHyperGParams,logical-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive<-,ListHyperGParams,logical-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
drive<-,miRNAListHyperGParams,logical-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
geneCounts,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneCounts,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneCounts,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneCounts,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneCounts,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneCounts,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdsByCategory,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdsByCategory,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdsByCategory,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdsByCategory,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdsByCategory,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdsByCategory,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdUniverse,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdUniverse,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdUniverse,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdUniverse,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdUniverse,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneIdUniverse,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneMappedCount,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneMappedCount,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneMappedCount,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneMappedCount,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneMappedCount,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
geneMappedCount,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
GeneralListHyperGParams |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
GeneralListHyperGParams-class |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
GeneralListHyperGResult |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
GeneralListHyperGResult-class |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
getFeatureMatrix |
A set of ISA modules |
getFeatureMatrix,ISAModules-method |
A set of ISA modules |
getFeatureNames |
A set of ISA modules |
getFeatureNames,ISAModules-method |
A set of ISA modules |
getFeatures |
A set of ISA modules |
getFeatures,ISAModules-method |
A set of ISA modules |
getFeatureScores |
A set of ISA modules |
getFeatureScores,ISAModules-method |
A set of ISA modules |
getFullFeatureMatrix |
A set of ISA modules |
getFullFeatureMatrix,ISAModules-method |
A set of ISA modules |
getFullSampleMatrix |
A set of ISA modules |
getFullSampleMatrix,ISAModules-method |
A set of ISA modules |
getNoFeatures |
A set of ISA modules |
getNoFeatures,ISAModules-method |
A set of ISA modules |
getNoSamples |
A set of ISA modules |
getNoSamples,ISAModules-method |
A set of ISA modules |
getOrganism |
A set of ISA modules |
getOrganism,ISAModules-method |
A set of ISA modules |
getSampleMatrix |
A set of ISA modules |
getSampleMatrix,ISAModules-method |
A set of ISA modules |
getSampleNames |
A set of ISA modules |
getSampleNames,ISAModules-method |
A set of ISA modules |
getSamples |
A set of ISA modules |
getSamples,ISAModules-method |
A set of ISA modules |
getSampleScores |
A set of ISA modules |
getSampleScores,ISAModules-method |
A set of ISA modules |
gograph |
Plot part of the Gene Ontology hierarchy |
gographPlot |
Plot part of the Gene Ontology hierarchy |
GOListHyperGParams |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
GOListHyperGParams-class |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
GOListHyperGResult |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
GOListHyperGResult-class |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
hasNA |
Expression Set, normalized for using with ISA |
hasNA,ISAExpressionSet-method |
Expression Set, normalized for using with ISA |
hasNA<- |
Expression Set, normalized for using with ISA |
hasNA<-,ISAExpressionSet-method |
Expression Set, normalized for using with ISA |
htmlReport,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
htmlReport,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
htmlReport,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
htmlReport,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
htmlReport,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
htmlReport,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
hyperGTest,CHRListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
hyperGTest,GeneralListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
hyperGTest,GOListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
hyperGTest,KEGGListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
hyperGTest,ListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
hyperGTest,miRNAListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
ISA |
Iterative Signature Algorithm on Gene Expression data |
ISA2heatmap |
Heatmap of a transcription module |
ISACHR |
Calculate chromosome enrichment for transcription modules |
ISAEnrichment |
Enrichment analysis for transcription modules, based on
user-defined categories |
ISAExpressionSet |
Expression Set, normalized for using with ISA |
ISAExpressionSet-class |
Expression Set, normalized for using with ISA |
ISAFilterRobust |
Robustness of ISA biclusters |
ISAGO |
Calculate Gene Ontology enrichment for transcription modules |
ISAHTML |
Create HTML summary pages from the result of modular analysis |
ISAHTMLModules |
Create HTML summary pages from the result of modular analysis |
ISAHTMLTable |
Create HTML summary pages from the result of modular analysis |
ISAIterate |
Perform the Iterative Signature Algorithm |
ISAKEGG |
Calculate KEGG Pathway enrichment for transcription modules |
ISAmiRNA |
Calculate (predicted) miRNA target enrichment for transcription
modules |
ISAmnplot |
Plot group means against each other, for an ISA module |
ISAModules |
A set of ISA modules |
ISAModules-class |
A set of ISA modules |
ISANormalize |
Normalize expression data for the Iterative Signature Algorithm |
ISARobustness |
Robustness of ISA biclusters |
ISASweep |
Create an ISA module tree |
ISASweepGraph |
Create an ISA module tree |
ISASweepGraphPlot |
Create an ISA module tree |
ISAUnique |
Remove duplicated ISA modules |
oddsRatios,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
oddsRatios,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
oddsRatios,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
oddsRatios,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
oddsRatios,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
oddsRatios,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
ontology,GOListHyperGParams-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
ontology,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
ontology<-,GOListHyperGParams,character-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation of multiple gene sets. |
overlap |
Overlap of ISA biclusters |
overlapPlot |
Overlap of ISA biclusters |
pData,ISAModules-method |
A set of ISA modules |
prenormalized |
Expression Set, normalized for using with ISA |
prenormalized,ISAExpressionSet-method |
Expression Set, normalized for using with ISA |
prenormalized<- |
Expression Set, normalized for using with ISA |
prenormalized<-,ISAExpressionSet-method |
Expression Set, normalized for using with ISA |
print.ISAexpPlot |
Expression matrix plots for ISA modules |
profilePlot |
Profile plots for ISA biclusters |
pvalues,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
pvalues,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
pvalues,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
pvalues,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
pvalues,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
pvalues,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
sampExprs |
Expression Set, normalized for using with ISA |
sampExprs,ISAExpressionSet-method |
Expression Set, normalized for using with ISA |
sampleNames,ISAModules-method |
A set of ISA modules |
sampleThreshold |
A set of ISA modules |
sampleThreshold,ISAModules-method |
A set of ISA modules |
seedData |
A set of ISA modules |
seedData,ISAModules-method |
A set of ISA modules |
sigCategories,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
sigCategories,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
sigCategories,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
sigCategories,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
sigCategories,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
sigCategories,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
summary,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
summary,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
summary,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
summary,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
summary,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
summary,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeCounts,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeCounts,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeCounts,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeCounts,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeCounts,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeCounts,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeMappedCount,CHRListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeMappedCount,GeneralListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeMappedCount,GOListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeMappedCount,KEGGListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeMappedCount,ListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |
universeMappedCount,miRNAListHyperGResult-method |
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
calculation for multiple gene sets |