Annotation for microarrays

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Documentation for package ‘annotate’ version 1.76.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A B C D E F G H I J K L M N O P R S T U W

-- A --

abstText	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
abstText-method	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
ACC2homology	DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
accessionToUID	A function to convert accession values to NCBI UIDs.
ACCNUMStats	Provides statistics on the types of ids used for the ACCNUM environment of a given data package
allValidKeys	Get or verify valid IDs for a package or OrgDb object.
allValidKeys-method	Get or verify valid IDs for a package or OrgDb object.
annotate-defunct	Defunct Functions in Package 'annotate'
annPkgName	Get annotation package name from chip name
aqListGOIDs	List GO Identifiers by GO Ontology
articleTitle	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
articleTitle-method	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
authors	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
authors-method	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.

-- B --

blastSequences	Run a blast query to NCBI for either a string or an entrez gene ID and then return a series of MultipleAlignment objects.
buildChromLocation	A function to generate an instantiation of a chromLocation class
buildPubMedAbst	A function to generate an instantiation of a pubMedAbst class

-- C --

checkArgs	A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
chrCats	Returns a list of chromosome locations from a MAP environment
chromInfo	Class chromLocation, a class for describing genes and their chromosome mappings.
chromInfo-method	Class chromLocation, a class for describing genes and their chromosome mappings.
chromLengths	Class chromLocation, a class for describing genes and their chromosome mappings.
chromLengths-method	Class chromLocation, a class for describing genes and their chromosome mappings.
chromLocation	Class chromLocation, a class for describing genes and their chromosome mappings.
chromLocation-class	Class chromLocation, a class for describing genes and their chromosome mappings.
chromLocs	Class chromLocation, a class for describing genes and their chromosome mappings.
chromLocs-method	Class chromLocation, a class for describing genes and their chromosome mappings.
chromNames	Class chromLocation, a class for describing genes and their chromosome mappings.
chromNames-method	Class chromLocation, a class for describing genes and their chromosome mappings.
clearRepository	Functions to add arbitrary repositories
compatibleVersions	function to check to see if the packages represented by the names passed have the same version number
createLLChrCats	Returns a list of chromosome locations from a MAP environment
createMAPIncMat	Returns a list of chromosome locations from a MAP environment

-- D --

dataSource	Class chromLocation, a class for describing genes and their chromosome mappings.
dataSource-method	Class chromLocation, a class for describing genes and their chromosome mappings.
dropECode	Drop GO labels for specified Evidence Codes

-- E --

entrezGeneByID	Create a Query String for an Entrez Gene Identifier
entrezGeneQuery	Create a Query String for Entrez Genes

-- F --

fileName	Classes to represent HTML pages
fileName-method	Classes to represent HTML pages
filterGOByOntology	Filter GO terms by a specified GO ontology
findChr4LL	A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
findNeighbors	A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
FramedHTMLPage	Classes to represent HTML pages
FramedHTMLPage-class	Classes to represent HTML pages
FramedHTMLPage-method	Classes to represent HTML pages

-- G --

genbank	A function to open the browser to Genbank with the selected gene.
genelocator	Defunct Functions in Package 'annotate'
geneSymbols	Class chromLocation, a class for describing genes and their chromosome mappings.
geneSymbols-method	Class chromLocation, a class for describing genes and their chromosome mappings.
getAnnMap	Get annotation map
getBoundary	A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
getCells	Functions to create hypertext links that can be placed in a table cell of a HTML file
getEG	Functions to deal with Data Packages
getEvidence	Get the Evidence codes for a set of GO terms.
getGI	Queries the NCBI database to obtain the sequence for a given GenBank Accession number
getGO	Functions to deal with Data Packages
getGOChildren	Functions to Access GO data.
getGOdesc	Functions to deal with Data Packages
getGOOntology	Functions to Access GO data.
getGOParents	Functions to Access GO data.
getGOTerm	Functions to Access GO data.
getGPLNames	Function to extract data from the GEO web site
getLL	Functions to deal with Data Packages
getOntology	Get GO terms for a specified ontology
getOrgNameNCode	Functions to map to organism IDs used by NCBI homology.
getPMID	Functions to deal with Data Packages
getPMInfo	extract publication details and abstract from annotate::pubmed function output
getQuery4Affy	Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4EN	Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4ENSEMBL	Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4FB	Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4GB	Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4LL	Defunct Functions in Package 'annotate'
getQuery4OMIM	Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4SP	Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4TR	Functions to create hypertext links that can be placed in a table cell of a HTML file
getQuery4UG	Functions to create hypertext links that can be placed in a table cell of a HTML file
getQueryLink	Functions to create hypertext links that can be placed in a table cell of a HTML file
getRepositories	Functions to add arbitrary repositories
getSAGEFileInfo	Function to extract data from the GEO web site
getSAGEGPL	Function to extract data from the GEO web site
getSEQ	Queries the NCBI database to obtain the sequence for a given GenBank Accession number
getSYMBOL	Functions to deal with Data Packages
getTDRows	Functions to create hypertext links that can be placed in a table cell of a HTML file
getUniqAnnItem	Functions to deal with Data Packages
getValidChr	A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
GO2heatmap	Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
GOmnplot	A function to plot by group means against each other.

-- H --

hasGOannote	Check for GO annotation
hgByChroms	A dataset to show the human genome base pair locations per chromosome.
hgCLengths	A dataset which contains the lengths (in base pairs) of the human chromosomes.
HGID2homology	DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
hgu95Achroloc	Annotation data for the Affymetrix HGU95A GeneChip
hgu95Achrom	Annotation data for the Affymetrix HGU95A GeneChip
hgu95All	Annotation data for the Affymetrix HGU95A GeneChip
hgu95AProbLocs	chromLocation instance hgu95AProbLocs, an example of a chromLocation object
hgu95Asym	Annotation data for the Affymetrix HGU95A GeneChip
homoACC	Class "homoData"
homoACC-method	Class "homoData"
homoData	Class "homoData"
homoData-class	Class "homoData"
homoHGID	Class "homoData"
homoHGID-method	Class "homoData"
homoLL	Class "homoData"
homoLL-method	Class "homoData"
homoOrg	Class "homoData"
homoOrg-method	Class "homoData"
homoPS	Class "homoData"
homoPS-method	Class "homoData"
homoType	Class "homoData"
homoType-method	Class "homoData"
homoURL	Class "homoData"
homoURL-method	Class "homoData"
HTMLPage	Classes to represent HTML pages
htmlpage	Functions to build HTML pages
HTMLPage-class	Classes to represent HTML pages
HTMLPage-method	Classes to represent HTML pages

-- I --

initialize-method	Classes to represent HTML pages
isValidKey	Get or verify valid IDs for a package or OrgDb object.
isValidKey-method	Get or verify valid IDs for a package or OrgDb object.

-- J --

journal	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
journal-method	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.

-- K --

KEGG2heatmap	Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
KEGG2heatmap-method	Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
KEGGmnplot	A function to plot by group means against each other.
KEGGmnplot-method	A function to plot by group means against each other.

-- L --

LL2homology	DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
lookUp	Functions to deal with Data Packages

-- M --

mainPage	Classes to represent HTML pages
mainPage-method	Classes to represent HTML pages
makeAnchor	A Function To Generate HTML Anchors
mapOrgs	Functions to map to organism IDs used by NCBI homology.

-- N --

nChrom	Class chromLocation, a class for describing genes and their chromosome mappings.
nChrom-method	Class chromLocation, a class for describing genes and their chromosome mappings.
neighborGeneFinder	Defunct Functions in Package 'annotate'

-- O --

organism	Convenience function for getting the organism from an object or package
organism-method	Class chromLocation, a class for describing genes and their chromosome mappings.
organism-method	Convenience function for getting the organism from an object or package
orgNameNCode	Class "homoData"

-- P --

p2LL	A function to map from probes to unique Entrez Gene IDs
pageText	Classes to represent HTML pages
pageText-method	Classes to represent HTML pages
pageTitle	Classes to represent HTML pages
pageTitle-method	Classes to represent HTML pages
pm.abstGrep	An interface to grep for PubMed abstracts.
pm.getabst	Obtain the abstracts for a set PubMed list.
pm.titles	Obtain the titles of the PubMed abstracts.
pmAbst2HTML	HTML Generation for PubMed Abstracts
pmid	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pmid-method	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pmid2MIAME	use web to populate MIAME instance with pubmed details
PMIDAmat	A function to compute the probe to PubMed id incidence matrix.
pmidQuery	A function to query PubMed
probesByLL	Defunct Functions in Package 'annotate'
probesToChrom	Class chromLocation, a class for describing genes and their chromosome mappings.
probesToChrom-method	Class chromLocation, a class for describing genes and their chromosome mappings.
pubDate	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubDate-method	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubmed	A function to open the browser to Pubmed with the selected gene.
pubMedAbst	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubMedAbst-class	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pubMedAbst-method	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
PWAmat	A function to compute the probe to KEGG pathway incidence matrix.

-- R --

readGEOAnn	Function to extract data from the GEO web site
readIDNAcc	Function to extract data from the GEO web site
readUrl	Function to extract data from the GEO web site

-- S --

serializeDataPkgEnvs	A Function To Serialize Environment
serializeEnv	A Function To Serialize Environment
setRepository	Functions to add arbitrary repositories
show-method	Classes to represent HTML pages
show-method	Class chromLocation, a class for describing genes and their chromosome mappings.
show-method	Class "homoData"
show-method	Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
sidePage	Classes to represent HTML pages
sidePage-method	Classes to represent HTML pages

-- T --

toFile	Classes to represent HTML pages
toFile-method	Classes to represent HTML pages
topPage	Classes to represent HTML pages
topPage-method	Classes to represent HTML pages

-- U --

UniGeneQuery	Create a Query String for a UniGene Identifier
updateSymbolsToValidKeys	Take a list of symbols and translate them into the best possible ID for a package.
usedChromGenes	A function to select used genes on a chromosome from an ExpressionSet.

-- W --

weightByConfi	A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID
whatACC	Provides statistics on the types of ids used for the ACCNUM environment of a given data package