# Integrated Interpretation of Genes

## Documentation for package ‘GeneAnswers’ version 1.8.0

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

## Help Pages

B C D E G H M P R S T

GeneAnswers-package | Integrated Interpretation of Genes

## -- B --

buildNet | build and display a network for given IDs and interaction Matrix

## -- C --

caBIO2entrez | map caBIO gene IDs to Entrez gene IDs
categoryNet | Plot Category Links
chartPlots | Pie Chart and Bar Plots
class:GeneAnswers | Class GeneAnswers: contain and describe the relationship between given gene data and specified category

## -- D --

DmIALite | Fly gene interaction matrix
DO | Several data objects related with DO (Disease Ontology) and its mapping to genes
DO.graph.closure.gene | Several data objects related with DO (Disease Ontology) and its mapping to genes
DO.graph.gene | Several data objects related with DO (Disease Ontology) and its mapping to genes
DO.terms | Several data objects related with DO (Disease Ontology) and its mapping to genes
DO2gene.map | Several data objects related with DO (Disease Ontology) and its mapping to genes
DOLite | Disease Ontology Annotation List
DOLiteTerm | Disease Ontology Annotation Vector
drawTable | Concept-Gene Networking Plotting

## -- E --

entrez2caBIO | map Entrez gene IDs to caBIO gene IDs

## -- G --

gene2DO.map | Several data objects related with DO (Disease Ontology) and its mapping to genes
geneAnnotationHeatmap | Make a concept-gene cross tabulation
GeneAnswers | Integrated Interpretation of Genes
GeneAnswers-class | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
geneAnswersBuilder | Build an object of a GeneAnswers class
geneAnswersChartPlots | Make pie chart and bar plot
geneAnswersConceptNet | Concept-Gene Networking Plotting
geneAnswersConceptRelation | Display a network related to given concepts for a GeneAnswers instance
geneAnswersConcepts | Concept-Gene Networking Plotting
geneAnswersHeatmap | Generate Concept-Gene Tabulates
geneAnswersHomoMapping | Mapping homogenes for a GeneAnswers instance
geneAnswersReadable | Make GeneAnswers Instance readable
geneAnswersSort | Sort enrichmentInfo of a GeneAnswers instance
geneConceptNet | Generate Concept-gene network
geneFunSummarize | Summarize gene functions (annotations) based collective annotation evidences associated with ontology terms
getAnnLib | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getAnnLib-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getcaBIOPATHList | Retrieve caBIO path categories containing given genes
getcaBIOPATHTerms | Get Pathway names of given REACTOME PATH_DB IDs
getCategoryList | Retrieve categories containing given genes
getCategoryTerms | Mapping Category IDs to Terms
getCategoryType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getCategoryType-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getConceptTable | Generate top concepts-genes table
getConnectedGraph | build and display a network for given IDs
getDOLiteTerms | Get DOLite Terms of Given DOLite IDs
getEnrichmentInfo | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getEnrichmentInfo-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getGeneExprProfile | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getGeneExprProfile-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getGeneInput | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getGeneInput-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getGenesInCategory | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getGenesInCategory-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getGOList | Get GO list of given genes
getHomoGeneIDs | Get homologous genes of given genes
getMultiLayerGraphIDs | retrieve multilayer interacted nodes for given IDs and interaction Matrix
getNextGOIDs | retrieve parents or children GO IDs for given GO IDs
getPATHList | Retrieve KEGG categories containing given genes
getPATHTerms | Get Pathway names of given KEGG IDs
getPValueT | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getPValueT-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getREACTOMEPATHList | Retrieve REACTOME path categories containing given genes
getREACTOMEPATHTerms | Get Pathway names of given REACTOME PATH_DB IDs
getSingleLayerGraphIDs | retrieve direct interacted nodes for given IDs and interaction Matrix
getSymbols | Convert entrez gene IDs to gene symbols
getTestType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getTestType-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getTotalGeneNumber | Obtain the total number of genes in the given annotation library
groupReport | Generate a multigroup Concepts-genes analysis report

## -- H --

HsIALite | Human gene interaction matrix
humanExpr | Example human expression data
humanGeneInput | Example human gene data

## -- M --

MmIALite | Mouse gene interaction matrix
mouseExpr | Example mouse expression data
mouseGeneInput | Example mouse gene data

## -- P --

plotGeneFunSummary | plot the summarized gene annotation (ontologies) of a gene
plotGraph | plot and render a graphNEL object
plotOntologyGraph | plot the ontology graph

## -- R --

RnIALite | Rat gene interaction matrix

## -- S --

sampleGroupsData | Example human expression data
saveGeneFunSummary | save the summarized gene function as a tab-separated text file
searchEntrez | Search specified information from Entrez site
setAnnLib | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setAnnLib-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setCategoryType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setCategoryType-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setEnrichmentInfo | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setEnrichmentInfo-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setGeneExprProfile | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setGeneExprProfile-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setGeneInput | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setGeneInput-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setGenesInCategory | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setGenesInCategory-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setPValueT | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setPValueT-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setTestType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setTestType-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
show | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
show-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
simplifyGeneFunSummary | Simplify the significant ontology terms to a miniSet annotation
summary | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
summary-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category

## -- T --

topcaBIO.PATH | Present top CABIO.PATH enrichment test information
topcaBIO.PATHGenes | Present top CABIO.PATH enrichment test information with genes
topCategory | Present top enrichment test information
topCategoryGenes | Present top enrichment test information with genes
topDOLITE | Present top DOLITE enrichment test information
topDOLITEGenes | Present top DOLITE enrichment test information with genes
topGO | Present top GO enrichment test information
topGOGenes | Present top GO enrichment test information with genes
topPATH | Present top KEGG enrichment test information
topPATHGenes | Present top KEGG enrichment test information with genes
topREACTOME.PATH | Present top REACTOME.PATH enrichment test information
topREACTOME.PATHGenes | Present top REACTOME.PATH enrichment test information with genes