Integrated Interpretation of Genes


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Documentation for package ‘GeneAnswers’ version 2.24.0

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B C D E G H M 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
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
getListGIF getListGIF
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

-- R --

RnIALite Rat gene interaction matrix

-- S --

sampleGroupsData Example human expression data
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
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