DatPkg-class: Class "DatPkg"

In Bioconductor/Category: Category Analysis

Class "DatPkg"

Description

DatPkg is a VIRTUAL class for representing annotation data packages.

AffyDatPkg is a subclass of DatPkg used to represent standard annotation data packages that follow the format of Affymetrix expression array annotation.

YeastDatPkg is a subclass of DatPkg used to represent the annotation data packages for yeast. The yeast chip packages are based on sgd and are internally different from the AffyDatPkg conforming packages.

ArabidopsisDatPkg is a subclass of DatPkg used to represent the annotation packages for Arabidopsis. These packages are internally slightly different from the AffyDatPkg conforming packages.

Org.XX.egDatPkg is a subclass of DatPkg used to represent the org.*.eg.db organism-level Entez Gene based annotation data packages.

OBOCollectionDatPkg is a subclass of DatPkg used to represent the OBO based annotation data packages.

GeneSetCollectionDatPkg is a subclass of DatPkg used to represent annotations in the form of GeneSetCollection objects which are not based on any annotation packages but are instead derived from custom (user supplied) annotations.

These methods have been extended to accommodate uninstalled annotation objects, primarily those available from the AnnotationHub package. See below for an example.

Objects from the Class

A virtual Class: No objects may be created from it.

Given the name of an annotation data package, DatPkgFactory can be used to create an appropriate DatPkg subclass.

Slots

name

A string giving the name of the annotation data package.

db

The underlying AnnotationDbi database object.

installed

Boolean. Distinguishes between conventional installed annotation packages, and those from AnnotationHub.

Methods

See showMethods(classes="DatPkg"). The set of methods, ID2EntreizID map between the standard IDs for an organism, or Chip and EntrezIDs, typically to give a way to get the GO terms. Different organisms, such as S. cerevisae and A. thaliana have their own internal IDs, so we need specialized methods for them.

Author(s)

Seth Falcon

Examples

DatPkgFactory("hgu95av2")
## Not run: 
DatPkgFactory("org.Sc.sgd")
DatPkgFactory("org.Hs.eg.db")
DatPkgFactory("ag")
library(AnnotationHub)
hub <- AnnotationHub()
## get an OrgDb for Atlantic salmon
query(hub, c("salmo salar","orgdb"))
salmodb <- hub[["AH58003"]]
DatPkgFactory(salmodb)

## End(Not run)

Bioconductor/Category documentation built on Oct. 29, 2023, 4:15 p.m.