Integrated Interpretation of Genes

Documentation for package ‘GeneAnswers’ version 1.10.0

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

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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