CollectionType-class {GSEABase}R Documentation

Class "CollectionType"

Description

These classes provides a way to tag the origin of a GeneSet. Collection types can be used in manipulating (e.g., selecting) sets, and can contain information specific to particular sets (e.g., category and subcategory classifications of BroadCollection.)

Objects from the Class

The following classes can tag gene sets; GO, KEGG, Chr, Chrloc, OMIM, and PMID collections can be derived from chip or organism ‘annotation’ packages.

NullCollection
No formal collection information available.
BroadCollection
Derived from, or destined to be, Broad XML. Usually created and written getBroadSets, toBroadXML.
ComputedCollection
A computationally created collection, e.g., by performing logic operations on gene sets.
ExpressionSetCollection
Derived from ExpressionSet. Usually created during a call to GeneSet or GeneColorSet.
GOCollection
Collection derived using Gene Ontology (GO) terms.
OBOCollection
Collection derived from GOCollection, specifically from files described by the OBO file format. See OBOCollection
KEGGCollection
Collection derived using KEGG terms.
ChrCollection
Collection derived using chromsome locations
ChrlocCollection
Collection derived using chromosome starting posistions
MapCollection
Collection derived from cytogenic bands.
OMIMCollection
Collection derived from identifiers in the Online Inheritance in Man.
PMIDCollection
Collection derived from PMID identifiers.
PfamCollection
Collection derived from Pfam identifiers.
PrositeCollection
Collection derived from Prosite identifiers.

Objects are instantiated with calls to CollectionType constructors, with slot names as possible arguments.

Slots

CollectionType classes (Null, ComputedCollection, ExpressionSet) have the slot:

type:
Object of class "ScalarCharacter" containing the character string representation of this CollectionType.

CollectionIdType classes (KEGG, OMIM, PMID, Chr, Chrloc, Map, GO) extend the CollectionType and have the additional slot:

ids:
Object of class "character" containing a vector of character string representations of corresponding identifiers, e.g., ‘KEGG’ or ‘GO’ terms.

GOCollection extends CollectionIdType and has the additional slot:

evidenceCode:
Object of class "character", containing GO evidence codes used to construct the gene set.

OBOCollection extends GOCollection; see OBOCollection.

BroadCollection has slots:

category:
Object of class "ScalarCharacter" containing terms from the Broad list of categories, or NA
subCategory:
Object of class "ScalarCharacter" containing Broad sub-categories, or NA

Methods

CollectionType classes have methods:

collectionType<-
signature(object = "GeneSet", value = "CollectionType"): Replace the CollectionType
collectionType
signature(object = "CollectionType"): Retrieve the collection type.
|, &, intersect, union, setdiff
signature(e1="CollectionType", e2="CollectionType"): return e1 when class(e1) and class(e2) are the same, or ComputedCollection when different.
show
signature(object = "CollectionType"): display the collection type.

CollectionIdType classes inherit CollectionType methods, and have in addition:

ids
signature(object="CollectionIdType"): Retrieve the identifiers of the collection type.
[
signature(object="CollectionIdType", i="missing", j="missing", ..., ids=ids(object)): return a subset of object containing only ids in ids
|, &, intersect, union, setdiff
signature(e1="CollectionIdType", e2="CollectionIdType"): always return ComputedCollection.

GOCollection inherits CollectionIdType methods, and has in addition:

evidenceCode
Retrieve the evidence codes of the GO collection. Evidence codes are summarize in, e.g., GOENTREZID.
[
signature(object="CollectionIdType", i="missing", j="missing", ..., evidenceCode=evidenceCode(object), ontology=ontology(object)): return a subset of object containing only evidence and ontology codes in evidenceCode, ontology. This method passes arguments ... to [,CollectionIdType methods.

BroadCollection has methods:

bcCategory
Retrieve the category of the Broad collection.
bcSubCategory
Retrieve the sub-category of the Broad collection.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

See Also

CollectionType consturctors.

Examples

names(getClass("CollectionType")@subclasses)

## Create a CollectionType and ask for its type
collectionType(ExpressionSetCollection())

## Not run: 
## Read two GeneSets from a Broad XML file into a list, verify that
## they are both BroadCollection's. Category / subcategory information
## is unique to Broad collections.
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
sets <- getBroadSets(fl)
sapply(sets, collectionType)
## End(Not run)

## ExpressionSets are tagged with ExpressionSetCollection; there is no
## 'category' information.
data(sample.ExpressionSet)
gs <- GeneSet(sample.ExpressionSet[100:109],
              setName="sample.GeneSet", setIdentifier="123")
collectionType(gs)

## GOCollections are created by reference to GO terms and evidenceCodes
GOCollection("GO:0005488")
## requires library(GO); EntrezIdentifers automatically created
## Not run: 
GeneSet(GOCollection(c("GO:0005488", "GO:0019825"),
                     evidenceCode="IDA"))
## End(Not run)

[Package GSEABase version 1.4.0 Index]