Expression data analysis via the Iterative Signature Algorithm

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Documentation for package ‘eisa’ version 1.32.0

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A C D E F G H I K L M O P R S U misc

-- A --

ALLModules ISA transcription modules for the ALL data
ALLModulesSmall ISA transcription modules for the ALL data
annotate Convert ISA modules to a Biclust object, or the opposite
annotation-method A set of ISA modules
anrichment Enrichment analysis for transcription modules, based on user-defined categories

-- C --

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-method Convert ISA modules to a Biclust object, or the opposite
condGeneIdUniverse-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
conditional-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
conditional-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
conditional<--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

-- D --

dim-method A set of ISA modules
drive Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
drive-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<--method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.

-- E --

expectedCounts-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
expPlot Expression matrix plots for ISA modules
expPlotColbar Expression matrix plots for ISA modules
expPlotCreate Expression matrix plots for ISA modules

-- F --

featExprs Expression Set, normalized for using with ISA
featExprs-method Expression Set, normalized for using with ISA
featureNames-method A set of ISA modules
featureThreshold A set of ISA modules
featureThreshold-method A set of ISA modules

-- G --

geneCounts-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
geneIdsByCategory-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
geneIdUniverse-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
geneMappedCount-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-method A set of ISA modules
getFeatureNames A set of ISA modules
getFeatureNames-method A set of ISA modules
getFeatures A set of ISA modules
getFeatures-method A set of ISA modules
getFeatureScores A set of ISA modules
getFeatureScores-method A set of ISA modules
getFullFeatureMatrix A set of ISA modules
getFullFeatureMatrix-method A set of ISA modules
getFullSampleMatrix A set of ISA modules
getFullSampleMatrix-method A set of ISA modules
getNoFeatures A set of ISA modules
getNoFeatures-method A set of ISA modules
getNoSamples A set of ISA modules
getNoSamples-method A set of ISA modules
getOrganism A set of ISA modules
getOrganism-method A set of ISA modules
getSampleMatrix A set of ISA modules
getSampleMatrix-method A set of ISA modules
getSampleNames A set of ISA modules
getSampleNames-method A set of ISA modules
getSamples A set of ISA modules
getSamples-method A set of ISA modules
getSampleScores A set of ISA modules
getSampleScores-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

-- H --

hasNA Expression Set, normalized for using with ISA
hasNA-method Expression Set, normalized for using with ISA
hasNA<- Expression Set, normalized for using with ISA
hasNA<--method Expression Set, normalized for using with ISA
htmlReport-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
hyperGTest-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.

-- I --

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

-- K --

KEGGListHyperGParams Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
KEGGListHyperGParams-class Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
KEGGListHyperGResult Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
KEGGListHyperGResult-class Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets

-- L --

length-method A set of ISA modules
ListHyperGParams Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
ListHyperGParams-class Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
ListHyperGResult Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
ListHyperGResult-class Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets

-- M --

makeValidParams-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
miRNAListHyperGParams Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
miRNAListHyperGParams-class Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
miRNAListHyperGResult Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
miRNAListHyperGResult-class Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
mnplot Plot group means against each other, for an ISA module

-- O --

oddsRatios-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
ontology-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
ontology-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
ontology<--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

-- P --

pData-method A set of ISA modules
prenormalized Expression Set, normalized for using with ISA
prenormalized-method Expression Set, normalized for using with ISA
prenormalized<- Expression Set, normalized for using with ISA
prenormalized<--method Expression Set, normalized for using with ISA
print.ISAexpPlot Expression matrix plots for ISA modules
profilePlot Profile plots for ISA biclusters
pvalues-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets

-- R --

runData A set of ISA modules
runData-method A set of ISA modules

-- S --

sampExprs Expression Set, normalized for using with ISA
sampExprs-method Expression Set, normalized for using with ISA
sampleNames-method A set of ISA modules
sampleThreshold A set of ISA modules
sampleThreshold-method A set of ISA modules
seedData A set of ISA modules
seedData-method A set of ISA modules
sigCategories-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
summary-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets

-- U --

universeCounts-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
universeMappedCount-method Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets

-- misc --

[-method A set of ISA modules
[[-method A set of ISA modules