Integrated Interpretation of Genes


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Documentation for package ‘GeneAnswers’ version 1.2.0

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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