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.

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.

### Author(s)

Martin Morgan <Martin.Morgan@RoswellPark.org>

### See Also

`CollectionType` consturctors; `getBroadSets` for importing collections from the Broad (and sources).

### Examples

    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)

[Package GSEABase version 1.54.0 Index]