# Integrated Interpretation of Genes

## Documentation for package ‘GeneAnswers’ version 1.2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

GeneAnswers-package | Integrated Interpretation of Genes
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
DOLite | Disease Ontology Annotation List
DOLiteTerm | Disease Ontology Annotation Vector
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
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
getAnnLib | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getAnnLib,GeneAnswers-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getCategoryList | Retrieve categories containing given genes
getCategoryTerms | Convert Category IDs to Terms
getCategoryType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getCategoryType,GeneAnswers-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getDOLiteTerms | Get DOLite Terms of Given DOLite IDs
getEnrichmentInfo | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getEnrichmentInfo,GeneAnswers-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,GeneAnswers-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,GeneAnswers-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,GeneAnswers-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
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,GeneAnswers-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getSymbols | Convert entrez gene IDs to gene symbols
getTestType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
getTestType,GeneAnswers-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
humanExpr | Example human expression data
humanGeneInput | Example human gene data
mouseExpr | Example mouse expression data
mouseGeneInput | Example mouse gene data
searchEntrez | Search specified information from Entrez site
setAnnLib | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
setAnnLib,GeneAnswers-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,GeneAnswers-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,GeneAnswers-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,GeneAnswers-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,GeneAnswers-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,GeneAnswers-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,GeneAnswers-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
summary | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
summary,GeneAnswers-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category
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