# Expression data analysis via the Iterative Signature Algorithm

## Documentation for package ‘eisa’ version 1.0.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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
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