CollectionType-class: 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.)

Arguments

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.
ontology: Object of class "character" vector of GO ontology terms used to filter GO terms in the GO Collection.

The values of evidenceCode are

Experimental Evidence Codes

EXP: Inferred from Experiment
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern

Computational Analysis Evidence Codes

ISS: Inferred from Sequence or Structural Similarity
ISO: Inferred from Sequence Orthology
ISA: Inferred from Sequence Alignment
ISM: Inferred from Sequence Model
IGC: Inferred from Genomic Context
RCA: inferred from Reviewed Computational Analysis

Author Statement Evidence Codes

TAS: Traceable Author Statement
NAS: Non-traceable Author Statement

Curator Statement Evidence Codes

IC: Inferred by Curator
ND: No biological Data available

Automatically-assigned Evidence Codes

IEA: Inferred from Electronic Annotation

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.
ontology: Retrieve the ontology terms of the GO collection.
[: 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.

Examples

Run this code

names(getClass("CollectionType")@subclasses)

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

## 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)

## 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)