Package 'annaffy'

Description

Dispatches requests for annotation data to the correct function. Alternatively returns a list of all the columns it supports.

Usage

aaf.handler(probeids, chip, name)

Arguments

Value

An aafList containing objects of the propper class.

If no arguments are passed, it will return a character vector of the columns currently supported.

Note

Written at the NASA Center for Computational Astrobiology
http://cca.arc.nasa.gov/

Author(s)

Colin A. Smith, [email protected]

Description

For the given probeids, constructs an aafList of aafChromLoc objects containing annotation data from the chip data package.

Usage

aafChromLoc(probeids, chip)

Arguments

Value

An aafList of aafChromLoc objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafChromLoc-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    locations <- aafChromLoc(probes, "hgu95av2.db")
    show(locations[6:10])
}

Description

An abstraction for gene chromosome locations from Bioconductor data packages.

Objects from the Class

Objects are generally created by the aafChromLoc constructor. Objects can also be created manually by calls of the form new("aafChromLoc", description).

Slots

.Data:

Object of class integer

Extends

Class integer, from data part.

Methods

No methods defined with class "aafChromLoc" in the signature. See generic implementations of getText, getURL, getHTML, getTD, and getCSS.

Author(s)

Colin A. Smith, [email protected]

See Also

aafChromLoc

Description

For the given probeids, constructs an aafList of aafChromosome objects containing annotation data from the chip data package.

Usage

aafChromosome(probeids, chip)

Arguments

Value

An aafList of aafChromosome objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafChromosome-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    chromosomes <- aafChromosome(probes, "hgu95av2.db")
    show(chromosomes[6:10])
}

Description

An abstraction for gene gene chromosome assignments from Bioconductor data packages.

Objects from the Class

Objects are generally created by the aafChromosome constructor. Objects can also be created manually by calls of the form new("aafChromosome", description).

Slots

.Data:

Object of class character

Extends

Class character, from data part.

Methods

No methods defined with class "aafChromosome" in the signature. See generic implementations of getText, getURL, getHTML, getTD, and getCSS.

Author(s)

Colin A. Smith, [email protected]

See Also

aafChromosome

Description

For the given probeids, constructs an aafList of aafCytoband objects containing annotation data from the chip data package.

Usage

aafCytoband(probeids, chip)

Arguments

Value

An aafList of aafCytoband objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafCytoband-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    bands <- aafCytoband(probes, "hgu95av2.db")
    show(bands[6:10])
}

Description

An abstraction for cytoband data from Bioconductor data packages.

Objects from the Class

Objects are generally created by the aafCytoband constructor. Objects can also be created manually by calls of the form new("aafCytoband", band, genbank).

Slots

band:

Object of class character containing genomic cytoband

gene:

Object of class character containing containing Gene ID

Methods

getText

(aafCytoband): Returns text of band.

getURL

(aafCytoband): Returns a URL corresponding entry in NCBI's cytoband map viewer.

See generic implementations of getHTML, getTD, and getCSS.

Author(s)

Colin A. Smith, [email protected]

See Also

aafCytoband

Description

For the given probeids, constructs an aafList of aafDescription objects containing annotation data from the chip data package.

Usage

aafDescription(probeids, chip)

Arguments

Value

An aafList of aafDescription objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafDescription-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    descriptions <- aafDescription(probes, "hgu95av2.db")
    show(descriptions[6:10])
}

Description

An abstraction for gene description from Bioconductor data packages.

Objects from the Class

Objects are generally created by the aafDescription constructor. Objects can also be created manually by calls of the form new("aafDescription", description).

Slots

.Data:

Object of class character

Extends

Class character, from data part.

Methods

No methods defined with class "aafDescription" in the signature. See generic implementations of getText, getURL, getHTML, and getTD.

Author(s)

Colin A. Smith, [email protected]

See Also

aafDescription

Description

Contains expression values for 250 probe ids with 8 samples. Two covariates are provided. Expression comes from the hgu95av2 chip.

Details

The data is real but anonymized. 250 genes expression values were chosen at random from an existing ExpressionSet. Another 250 probe ids were selected at random and were assigned to the expression values. That way, expression values do not correspond to the true probe ids.

Post-processing was done with rma() in affy 1.2.23.

Description

For the given probeids, constructs an aafList of aafGenBank objects containing annotation data from the chip data package.

Usage

aafGenBank(probeids, chip)

Arguments

Value

An aafList of aafGenBank objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafGenBank-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    gbs <- aafGenBank(probes, "hgu95av2.db")
    show(gbs[6:10])
}

Description

An abstraction for GenBank accession numbers from Bioconductor data packages.

Objects from the Class

Objects are generally created by the aafGenBank constructor. Objects can also be created manually by calls of the form new("aafGenBank", accnum).

Slots

.Data:

Object of class character

Extends

Class character, from data part.

Methods

getURL

(aafGenBank): Returns a URL to the corresponding entry in NCBI's GenBank database.

See generic implementations of getText, getHTML, and getTD.

Author(s)

Colin A. Smith, [email protected]

See Also

aafGenBank

Description

For the given probeids, constructs an aafList of aafGO objects containing annotation data from the chip data package.

Usage

aafGO(probeids, chip)

Arguments

Value

An aafList of aafGO objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafGO-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    gos <- aafGO(probes, "hgu95av2.db")
    show(gos[6:10])
}

Description

An abstraction for gene ontology ids from Bioconductor data packages. This class is actually extends aafList and holds aafGOItem objects which have the actual annotation data.

Objects from the Class

Objects are generally created by the aafGO constructor. Objects can also be created manually by calls of the form new("aafGO", list(goitems)).

Slots

.Data:

Object of class list

Extends

Class aafList, from data part.

Methods

getText

(aafGO): Returns a comma delimeted list of the individual aafGOItem objects.

getURL

(aafGO): Returns a single URL to an AmiGO page which displays all the gene ontology identifiers in an hierarchical listing.

getHTML

(aafGO): Returns an HTML representation of each of the individual aafGOItem objects, concatenated together.

getTD

(aafGO): Returns an HTML table cell representation with the class set to "aafGO".

getCSS

(aafGOItem): Returns a line of CSS that indents GOItem paragraphs.

Author(s)

Colin A. Smith, [email protected]

See Also

aafGO, aafGOItem, aafList

Description

An abstraction for gene ontology id elements from Bioconductor data packages. Multiple instances of this class are held by the wrapper class aafGO.

Objects from the Class

Objects are generally created by the aafGO constructor. Objects can also be created manually by calls of the form new("aafGOItem", id, name, type).

Slots

id:

Object of class character containing GO id

name:

Object of class character containing textual name

type:

Object of class character containing GO subtype

evid:

Object of class character containing GO evidence code

Methods

getText

(aafGOItem): Returns textual representation formatted "id: name".

getURL

(aafGOItem): Returns a URL to the corresponding gene ontology entry on AmiGO.

getHTML

(aafGOItem): Returns an HTML representation including the URL link, gene ontology name, and rollover subtype.

Author(s)

Colin A. Smith, [email protected]

See Also

aafGO-class, aafGO

Description

A class for displaying gene expression values with a green background of differing intensities.

Objects from the Class

Objects are generally created by the aafTableInt constructor. Objects can also be created manually by calls of the form new("aafIntensity", intensity).

Slots

.Data:

Object of class numeric

Extends

Class numeric, from data part.

Methods

getTD

(aafIntensity): Returns an HTML table cell with background varrying from white to green depending on intensity. Scaling is controlled by two options, minIntensity (fully white) and maxIntensity (fully green), usually set by writeHTML.

See generic implementations of getText, getURL, getHTML, and getCSS.

Author(s)

Colin A. Smith, [email protected]

See Also

aafTableInt

Description

A class for lists of annotation data objects.

Objects from the Class

Objects are generally created by any of the annotation data constructors that are also part of this package. Objects can also be created manually by calls of the form new("aafList", list).

Slots

.Data:

Object of class list

Extends

Class list, from data part.

Methods

getText

(aafList): Returns a character vector containing textual representations of every item.

getURL

(aafList): Returns a character vector containing single URLs (if possible) of every item.

getHTML

(aafList): Returns a character vector containing HTML representations of every item.

getTD

(aafList): Returns a character vector containing HTML table cell representations of every item.

getCSS

(aafList): Returns getCSS() of the first item in the list.

[

(aafList): Returns a subset of aafList as another aafList object.

Author(s)

Colin A. Smith, [email protected]

Description

For the given probeids, constructs an aafList of aafLocusLink objects containing annotation data from the chip data package.

Usage

aafLocusLink(probeids, chip)

Arguments

Value

An aafList of aafLocusLink objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafLocusLink-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    lls <- aafLocusLink(probes, "hgu95av2.db")
    show(lls[6:10])
}

Description

An abstraction for LocusLink ids from Bioconductor data packages.

Objects from the Class

Objects are generally created by the aafLocusLink constructor. Objects can also be created manually by calls of the form new("aafLocusLink", id).

Slots

.Data:

Object of class integer

Extends

Class integer, from data part.

Methods

getURL

(aafLocusLink): Returns a URL to the corresponding entry in NCBI's LocusLink database. On the rare chance that more than one id is defined, more than one URL will be returned.

See generic implementations of getText, getHTML, and getTD.

Author(s)

Colin A. Smith, [email protected]

See Also

aafLocusLink

Description

For the given probeids, constructs an aafList of aafPathway objects containing annotation data from the chip data package.

Usage

aafPathway(probeids, chip)

Arguments

Value

An aafList of aafPathway objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafPathway-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    pathways <- aafPathway(probes, "hgu95av2.db")
    show(pathways[6:10])
}

Description

An abstraction for KEGG pathway ids from Bioconductor data packages. This class is actually extends aafList and holds aafPathwayItem objects which have the actual annotation data.

Objects from the Class

Objects are generally created by the aafPathway constructor. Objects can also be created manually by calls of the form new("aafPathway", list(pathwayitems)).

Slots

.Data:

Object of class list

Extends

Class aafList, from data part.

Methods

getText

(aafGO): Returns a comma delimeted list of the individual aafPathwayItem objects.

getURL

(aafGO): Returns zero length character vector because this method is not valid for this class.

getHTML

(aafGO): Returns an HTML representation of each of the individual aafPathwayItem objects, concatenated together.

getTD

(aafGO): Returns an HTML table cell representation with the class set to "aafPathway".

getCSS

(aafGO): Returns a line of CSS which intends PathwayItem paragraphs.

Author(s)

Colin A. Smith, [email protected]

See Also

aafPathway, aafPathwayItem, aafList

Description

An abstraction for KEGG pathway id elements from Bioconductor data packages. Multiple instances of this class are held by the wrapper class aafPathway.

Objects from the Class

Objects are generally created by the aafPathway constructor. Objects can also be created manually by calls of the form new("aafPathwayItem", id, name, enzyme).

Slots

id:

Object of class character containing KEGG pathway id

name:

Object of class character containing textual name (no longer supported)

enzyme:

Object of class character containing the Enzyme Commision number if applicable

Methods

getText

(aafPathwayItem): Returns textual representation formatted "id: name".

getURL

(aafPathwayItem): Returns a URL to the corresponding entry in the Kyoto Encyclopedia of Genes and Genomes database. If there is a corresponding EC number, it will be highlighted in red.

getHTML

(aafPathwayItem): Returns an HTML representation including the URL link and pathway name.

Author(s)

Colin A. Smith, [email protected]

See Also

aafPathway-class, aafPathway

Description

For the given probeids, constructs an aafList of aafProbe objects.

Usage

aafProbe(probeids)

Arguments

Value

An aafList of aafProbe objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafProbe-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    probesets <- aafProbe(probes)
    getURL(probesets[6:10])
}

Description

An abstraction for Affymetrix ProbeSet ids.

Objects from the Class

Objects are generally created by the aafProbe constructor. Objects can also be created manually by calls of the form new("aafProbe", id).

Slots

.Data:

Object of class character

Extends

Class character, from data part.

Methods

getURL

(aafProbe): Returns a URL to the annotation found in the Affymetrix NetAffx Analysis Center.

See generic implementations of getText, getHTML, and getTD.

Author(s)

Colin A. Smith, [email protected]

See Also

aafProbe

Description

For the given probeids, constructs a list of aafPubMed objects containing annotation data from the chip data package.

Usage

aafPubMed(probeids, chip)

Arguments

Value

An aafList of aafPubMed objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafPubMed-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    pmids <- aafPubMed(probes, "hgu95av2.db")
    show(pmids[6:10])
}

Description

An abstraction for LocusLink ids from Bioconductor data packages.

Objects from the Class

Objects are generally created by the aafPubMed constructor. Objects can also be created manually by calls of the form new("aafPubMed", id).

Slots

.Data:

Object of class integer

Extends

Class integer, from data part.

Methods

getURL

(aafPubMed): Returns a single URL to the corresponding abstracts in NCBI's PubMed database.

getHTML

(aafPubMed): Returns an HTML link along with the number of abstracts.

getTD

(aafPubMed): Returns an HTML table cell representation with the class set to "aafPubMed".

getCSS

(aafPubMed): Returns a line of CSS which centers the PubMed link.

Author(s)

Colin A. Smith, [email protected]

See Also

aafPubMed

Description

Searches Gene Ontology ids for corresponding probe ids in a given chip, optionally including descendents.

Usage

aafSearchGO(chip, ids, descendents = TRUE, logic = "OR")

Arguments

Value

A character vector of probe ids matching the search criteria.

Author(s)

Colin A. Smith, [email protected]

See Also

aafSearchText

Description

Searches Bioconductor metadata annotation package text for specific strings or Perl compatible regular expressions.

Usage

aafSearchText(chip, colnames, text, logic = "OR")

Arguments

Value

A character vector of probe ids matching the search criteria.

Author(s)

Colin A. Smith, [email protected]

See Also

aafSearchGO

Examples

if (require(hgu95av2.db)) {
    aafSearchText("hgu95av2.db", "Description", c("kinase", "interferon"))
#   aafSearchText("hgu95av2.db", c("Gene Ontology", "Pathway"), "ribosome")
}

Description

A class for displaying signed numerical data with different styles depending on the sign.

Objects from the Class

Objects are generally created by the aafTable constructor. Objects can also be created manually by calls of the form new("aafSigned", signedval).

Slots

.Data:

Object of class numeric

Extends

Class numeric, from data part.

Methods

getTD

(aafSigned): Returns an HTML table cell with class differentially set based on sign. aafSignedPos is used for positive values. aafSignedNeg is used for negative values. aafSignedZero is used for zero values.

getCSS

(aafSigned): Returns two lines of CSS that set the cell background of positive values light blue and negative values light red.

See generic implementations of getText, getURL, and getHTML.

Author(s)

Colin A. Smith, [email protected]

See Also

aafTable

Description

For the given probeids, constructs a list of aafSymbol objects containing annotation data from the chip data package.

Usage

aafSymbol(probeids, chip)

Arguments

Value

An aafList of aafSymbol objects. NA values are returned as empty objects.

Author(s)

Colin A. Smith, [email protected]

See Also

aafSymbol-class

Examples

if (require(hgu95av2.db)) {
    data(aafExpr)
    probes <- featureNames(aafExpr)
    symbols <- aafSymbol(probes, "hgu95av2.db")
    show(symbols[6:10])
}

Description

An abstraction for gene symbol from Bioconductor data packages.

Objects from the Class

Objects are generally created by the aafSymbol constructor. Objects can also be created manually by calls of the form new("aafSymbol", description).

Slots

.Data:

Object of class character with gene symbol

Extends

Class character, from data part.

Methods

No methods defined with class "aafSymbol" in the signature. See generic implementations of getText, getURL, getHTML, and getTD.

Author(s)

Colin A. Smith, [email protected]

See Also

aafSymbol

Description

Constructs an aafTable object given vectors, lists, or aafList objects.

Usage

aafTable(..., items = list(...), colnames = names(items), 
         probeids = character(0), signed = FALSE)

Arguments

Value

An aafTable object.

Author(s)

Colin A. Smith, [email protected]

See Also

aafTable-class

Description

A class for storing and flexible output of microarray data to HTML and text formats.

Objects from the Class

Objects are generally created by any of the annotation table constructors that are also part of this package. Objects can also be created manually by calls of the form new("aafList", probeids, table).

Slots

probeids:

Object of class character containing the probe ids for each row of the table.

table:

Object of class list containing aafList objects all of the same length, representing the columns of the table. Each item in the list must have a unique name.

Methods

probeids

(aafTable): Returns a character vector containing the probe ids for each row of the table.

probeids<-

(aafTable): Sets the probe ids for the table rows. Can be set to character(0) if unknown or not applicable.

colnames

(aafTable): Returns a character vector containing the names of the columns stored in the table.

colnames<-

(aafTable): Set the column names for the table. Each must be unique.

dim

(aafTable): Returns the dimensions of the table.

merge

(aafTable, aafTable, all = FALSE, all.x = all, all.y = all, suffixes = c(".x",".y")): Merges two tables together, aligning common probe ids if possible. Duplicate column names are given suffixes to make them unique. Returns the merged table.

rbind

(aafTable, aafTable, ...): Vertically combines tables by row. Requires that column names be identical and that all tables either have probe ids defined or not.

[

Returns a subset of the table based on [row, column]. Indices may be passed as integers or probe ids/column names.

[[

Returns the given table column. This also supports recursive subsetting to address columns, then cells, then sub-cells (if applicable). See Extract for more information.

\$

Returns the given table column.

saveHTML

(aafTable, filename, title = "Bioconductor Affymetrix Probe Listing", colnames = colnames(aafTable), range = 1:dim(aafTable)[1], open = FALSE, widget = FALSE): Saves the table to HTML with the specified filename and title. Both the columns and the range of table rows can be specified. Range can either be specified as a character vector of probe ids or an integer vector of row positions. One can also specify whether to open the resulting file in the browser and whether to use a widget for column selection.

saveText

(aafTable, filename, header = TRUE, colnames = colnames(aafTable), range = 1:dim(aafTable)[1], widget = FALSE): Saves the table to tab delimited text with specified filename and optional header. Both the columns and the range of table rows can be specified. Range can either be specified as a character vector of probe ids or an integer vector of row positions. One can also specify whether to use a widget for column selection.

Author(s)

Colin A. Smith, [email protected]

See Also

aafTable, aafTableFrame, aafTableAnn, aafTableInt

Description

Constructs an aafTable object given a set of probe ids and desired annotation types.

Usage

aafTableAnn(probeids, chip, colnames = aaf.handler(chip = chip), widget = FALSE)

Arguments

Value

An aafTable object.

Author(s)

Colin A. Smith, [email protected]

See Also

aafTable-class

Description

Constructs an aafTable object given a data frame.

Usage

aafTableFrame(frame, colnames = names(frame), probeids = row.names(frame), 
              signed = FALSE)

Arguments

Value

An aafTable object.

Author(s)

Colin A. Smith, [email protected]

See Also

aafTable-class

Description

Constructs an aafTable object containing expression values given an ExpressionSet.

In the resulting HTML table, the expression values will have backgrounds with varying intensities of green depending on the expression measure.

Usage

aafTableInt(exprSet, colnames = sampleNames(exprSet), 
            probeids = featureNames(exprSet))

Arguments

Value

An aafTable object.

Author(s)

Colin A. Smith, [email protected]

See Also

aafTable-class, aafIntensity

Description

Methods to get relevant stylesheet lines for an object.

Methods

object = ANY

Returns an empty character vector.

Note

For information about other implementations of this method, see documentation of the respective class.

See Also

aafList-class, aafPubMed-class, aafGO-class, aafPathway-class, aafSigned-class

Description

Methods to get an HTML representation of an object.

Methods

object = ANY

Returns text of object along with URL link if applicable. If object is floating point, it displays a fixed number of significant digits as specified by the sigfigs option (default 6).

Note

For information about other implementations of this method, see documentation of the respective class.

See Also

aafList-class, aafPubMed-class, aafGO-class, aafGOItem-class, aafPathway-class, aafPathwayItem-class

Description

Methods to get an HTML table cell representation of an object.

Methods

object = ANY

Returns <td> tag containing HTML representation of object. Sets class attribute to class(object).

Note

For information about other implementations of this method, see documentation of the respective class.

See Also

aafList-class, aafGO-class, aafPathway-class, aafIntensity-class

Description

Methods to get a textual representation of an object.

Methods

object = ANY

Returns a comma delimeted list of the elements in list.

Note

For information about other implementations of this method, see documentation of the respective class.

See Also

aafList-class, aafCytoband-class, aafGO-class, aafGOItem-class, aafPathway-class, aafPathwayItem-class

Description

Methods to get a URL link to a web resource for an object.

Methods

object = ANY

Returns an empty character vector.

Note

For information about other implementations of this method, see documentation of the respective class.

See Also

aafList-class, aafGenBank-class, aafLocusLink-class, aafCytoband-class, aafUniGene-class, aafPubMed-class, aafGO-class, aafGOItem-class, aafPathwayItem-class

Description

Checks to see that the given packages contain all the necessary annotation environments to be usable by annaffy.

Usage

is.annpkg(packages, lib.loc = NULL)

Arguments

Value

A logical vector indicating whether the packages contain annotation data.

Author(s)

Colin A. Smith, [email protected]

Examples

pkgnames <- installed.packages()[,"Package"]
pkgnames <- pkgnames[1:5]
pkgnames[is.annpkg(pkgnames)]

Description

Presents the user with a dialog box to select items from a list.

Usage

selectorWidget(options, selected = character(0), title = "Selector",
               ordersel = FALSE, ordernsel = FALSE, 
               height = max(10,min(20,length(options))))

Arguments

Value

A character vector containing the selected items. If a vector of a different class was initially provided, it must be manually coerced back to the correct type.

Author(s)

Colin A. Smith, [email protected]