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 AffyDataPkg 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.

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.

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.

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")

## End(Not run)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Category)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Category/DatPkg-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DatPkg-class
> ### Title: Class "DatPkg"
> ### Aliases: DatPkg-class AffyDatPkg-class YeastDatPkg-class
> ###   Org.XX.egDatPkg-class GeneSetCollectionDatPkg DatPkgFactory
> ###   DatPkgFactory,character-method ID2GO ID2KEGG ID2EntrezID GO2AllProbes
> ###   KEGG2AllProbes ID2GO,DatPkg-method
> ###   ID2GO,GeneSetCollectionDatPkg-method ID2KEGG,DatPkg-method
> ###   ID2KEGG,GeneSetCollectionDatPkg-method ID2EntrezID,AffyDatPkg-method
> ###   ID2EntrezID,YeastDatPkg-method ID2EntrezID,Org.XX.egDatPkg-method
> ###   ID2EntrezID,ArabidopsisDatPkg-method
> ###   ID2EntrezID,GeneSetCollectionDatPkg-method GO2AllProbes,DatPkg-method
> ###   GO2AllProbes,YeastDatPkg-method GO2AllProbes,Org.XX.egDatPkg-method
> ###   GO2AllProbes,GeneSetCollectionDatPkg-method
> ###   KEGG2AllProbes,DatPkg-method
> ###   KEGG2AllProbes,GeneSetCollectionDatPkg-method
> ###   isDBDatPkg,DatPkg-method isDBDatPkg,GeneSetCollectionDatPkg-method
> ###   organism,DatPkg-method organism,GeneSetCollectionDatPkg-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> DatPkgFactory("hgu95av2")
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


An object of class "AffyDatPkg"
Slot "name":
[1] "hgu95av2"

> ## Not run: 
> ##D DatPkgFactory("org.Sc.sgd")
> ##D DatPkgFactory("org.Hs.eg.db")
> ##D DatPkgFactory("ag")
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>