Annotation for microarrays


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Documentation for package `annotate' version 1.8.0

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A B C D 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,pubMedAbst-method Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
abstUrl Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
abstUrl,pubMedAbst-method Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
ACC2homology 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
articleTitle Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
articleTitle,pubMedAbst-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,pubMedAbst-method Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.

-- B --

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 LocusLink id
chromInfo Class chromLocation, a class for describing genes and their chromosome mappings.
chromInfo,chromLocation-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,chromLocation-method 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,chromLocation-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,chromLocation-method Class chromLocation, a class for describing genes and their chromosome mappings.
compatibleVersions function to check to see if the packages represented by the names passed have the same version number

-- D --

dataSource Class chromLocation, a class for describing genes and their chromosome mappings.
dataSource,chromLocation-method Class chromLocation, a class for describing genes and their chromosome mappings.
Definition Class "GOTerms"
Definition,GOTerms-method Class "GOTerms"

-- F --

fileName Classes to represent HTML pages
fileName,HTMLPage-method Classes to represent HTML pages
findChr4LL A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id
findNeighbors A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id
FramedHTMLPage Classes to represent HTML pages
FramedHTMLPage,HTMLPage-method Classes to represent HTML pages
FramedHTMLPage-class Classes to represent HTML pages

-- G --

genbank A function to open the browser to Genbank with the selected gene.
genelocator A function to identify genes by their LocusLink (or other id).
geneSymbols Class chromLocation, a class for describing genes and their chromosome mappings.
geneSymbols,chromLocation-method Class chromLocation, a class for describing genes and their chromosome mappings.
getBoundary A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id
getCells Functions to create hypertext links that can be placed in a table cell of a HTML file
getGI Queries the NCBI database to obtain the sequence for a given GenBank Accession number
getGO Functions to deal with Data Packages
getGOdesc Functions to deal with Data Packages
getGPLNames Function to extract data from the GEO web site
getLL Functions to deal with Data Packages
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
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 Functions to create hypertext links that can be placed in a table cell of a HTML file
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
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
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 LocusLink id
GO2heatmap Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.
GOID Class "GOTerms"
GOID,GOTerms-method Class "GOTerms"
GOmnplot A function to plot by group means against each other.
GOTerms Class "GOTerms"
GOTerms-class Class "GOTerms"

-- H --

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 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,homoData-method Class "homoData"
homoData Class "homoData"
homoData-class Class "homoData"
homoHGID Class "homoData"
homoHGID,homoData-method Class "homoData"
homoLL Class "homoData"
homoLL,homoData-method Class "homoData"
homoOrg Class "homoData"
homoOrg,homoData-method Class "homoData"
homoPS Class "homoData"
homoPS,homoData-method Class "homoData"
homoType Class "homoData"
homoType,homoData-method Class "homoData"
homoURL Class "homoData"
homoURL,homoData-method Class "homoData"
HTMLPage Classes to represent HTML pages
htmlpage Functions to build HTML pages
HTMLPage,HTMLPage-method Classes to represent HTML pages
HTMLPage-class Classes to represent HTML pages

-- I --

initialize,FramedHTMLPage-method Classes to represent HTML pages
installDataPackage A function to install data packages from the Internet

-- J --

journal Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
journal,pubMedAbst-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.
KEGGmnplot A function to plot by group means against each other.

-- L --

LL2homology Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs
locuslinkByID A function to open the browser to Locuslink with the selected gene.
locuslinkQuery A function to open the browser to Locuslink using a provided search query.
lookUp Functions to deal with Data Packages

-- M --

mainPage Classes to represent HTML pages
mainPage,FramedHTMLPage-method Classes to represent HTML pages
mainPage,HTMLPage-method Classes to represent HTML pages
makeAnchor A Function To Generate HTML Anchors

-- N --

nChrom Class chromLocation, a class for describing genes and their chromosome mappings.
nChrom,chromLocation-method Class chromLocation, a class for describing genes and their chromosome mappings.
neighborGeneFinder A widget for locating genes neighboring a target gene

-- O --

Ontology Class "GOTerms"
Ontology,ANY-method Class "GOTerms"
Ontology,GOTerms-method Class "GOTerms"
organism Class chromLocation, a class for describing genes and their chromosome mappings.
organism,chromLocation-method Class chromLocation, a class for describing genes and their chromosome mappings.
orgNameNCode Class "homoData"

-- P --

p2LL A function to map from probes to unique Entrez Gene IDs
pageText Classes to represent HTML pages
pageText,HTMLPage-method Classes to represent HTML pages
pageTitle Classes to represent HTML pages
pageTitle,HTMLPage-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,pubMedAbst-method Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
pmidQuery A function to query PubMed
probesByLL A function that does reverse the mappings between probe ids and the corresponding values
probesToChrom Class chromLocation, a class for describing genes and their chromosome mappings.
probesToChrom,chromLocation-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,pubMedAbst-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,pubMedAbst-method 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.
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
revBase Functions to create anti-sense DNA string
revString Functions to create anti-sense DNA string

-- S --

Secondary Class "GOTerms"
Secondary,GOTerms-method Class "GOTerms"
serializeDataPkgEnvs A Function To Serialize Environment
serializeEnv A Function To Serialize Environment
show,chromLocation-method Class chromLocation, a class for describing genes and their chromosome mappings.
show,FramedHTMLPage-method Classes to represent HTML pages
show,GOTerms-method Class "GOTerms"
show,homoData-method Class "homoData"
show,HTMLPage-method Classes to represent HTML pages
show,pubMedAbst-method Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.
sidePage Classes to represent HTML pages
sidePage,FramedHTMLPage-method Classes to represent HTML pages
sidePage,HTMLPage-method Classes to represent HTML pages
Synonym Class "GOTerms"
Synonym,GOTerms-method Class "GOTerms"

-- T --

Term Class "GOTerms"
Term,GOTerms-method Class "GOTerms"
toFile Classes to represent HTML pages
toFile,FramedHTMLPage-method Classes to represent HTML pages
toFile,HTMLPage-method Classes to represent HTML pages
topPage Classes to represent HTML pages
topPage,FramedHTMLPage-method Classes to represent HTML pages
topPage,HTMLPage-method Classes to represent HTML pages

-- U --

UniGeneQuery Create a Query String for a UniGene Identifier
usedChromGenes A function to select used genes on a chromosome from an exprSet.

-- W --

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