Annotation for microarrays


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Documentation for package `annotate' version 1.4.0

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A B C D F G H I J L M N O P 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.
accessionToUID A function to convert accession values to NCBI UIDs.
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.

-- 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.

-- 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
getGO Functions to deal with Data Packages
getGOdesc Functions to deal with Data Packages
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
getQuery4LL 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
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

-- 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.
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
HTMLPage Classes to represent 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.

-- L --

ll.htmlpage Turn LocusLink ID's into a Clickable Web Page
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 --

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.

-- P --

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 groups probe ids by LocusLink ids
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.

-- S --

show,chromLocation-method Class chromLocation, a class for describing genes and their chromosome mappings.
show,FramedHTMLPage-method Classes to represent HTML pages
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

-- T --

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