GeneSetCollection-methods: Methods to construct GeneSetCollection instances

GeneSetCollection-methodsR Documentation

Methods to construct GeneSetCollection instances

Description

Use GeneSetCollection to construct a collection of gene sets from GeneSet arguments, or a list of GeneSets.

Usage

GeneSetCollection(object, ..., idType, setType)

Arguments

object

An argument determining how the gene set collection will be created, as described in the methods section.

...

Additional arugments for gene set collection construction, as described below.

idType

An argument of class GeneIdentifierType, used to indicate how the geneIds will be represented.

setType

An argument of class CollectionType, used to indicate how the collection is created.

Methods

signature(object = "GeneSet",idType="missing", setType="missing")

Construct a gene set collection from one or more GeneSet arugments.

signature(object = "list", idType="missing", setType="missing")

Construct a gene set collection from a list of GeneSets.

signature(object="missing", idType="AnnotationIdentifier", setType="CollectionType")
signature(object="missing", idType="AnnotationIdentifier", setType="CollectionIdType")

Construct a gene set collection of CollectionType entities (e.g., pathways for KEGGCollection, protein families for PfamCollection) implied by the map found in annotation(idType). If setType is a CollectionIdType and length(ids(setType))>0, the gene set collection is filtered to contain only those sets implied by the ids.

signature(object="character", idType="AnnotationIdentifier", setType="CollectionType")
signature(object="character", idType="AnnotationIdentifier", setType="CollectionIdType")
signature(object="character", idType="AnnotationIdentifier", setType="GOCollection")

Construct a gene set collection of CollectionType entities (e.g., pathways for KEGGCollection, protein families for PfamCollection) implied by the map found in annotation(idType). Use only those identifiers in object. If setType is a CollectionIdType and length(ids(setType))>0, the gene set collection is filtered to contain only those sets implied by the ids.

signature(object="character", idType="AnnotationIdentifier", setType="PfamCollection")

Construct a gene set collection by mapping all values in object to PfamIds found in the PFAM map implied by idType.

signature(object="character", idType="AnnotationIdentifier", setType="PrositeCollection")

Construct a gene set collection by mapping all values in object to ipi_ids found in the PFAM map implied by idType.

signature(object="character", idType="AnnotationIdentifier", setType="ChrlocCollection")

Construct a gene set collection by mapping all values in object to chromosome, strand, and position information found in the map implied by idType.

signature(object="ExpressionSet", idType="missing", setType="CollectionType")
signature(object="ExpressionSet", idType="missing", setType="CollectionIdType")

Construct a gene set collection using the annotation and featureNames of object to identify elements for CollectionType gene sets (e.g., pathways for KEGGCollection, protein families for PfamCollection) implied by object. The gene set collection contains only those AnnotationIdentifiers found in featureNames(object); if setType is a CollectionIdType and length(ids(setType))>0, the gene set collection is further filtered to contain only those sets implied by the ids.

signature(object="ExpressionSet", idType="missing", setType="GOCollection")

Construct a gene set collection using the annotation and featureNames of object to identify GO pathways implied by object. The map between featureNames and GO pathway identifiers is derived from the GO2PROBE table of the annotation package of object. The gene set collection contains only those AnnotationIdentifiers found in featureNames(object). The evidenceCode of GOCollection can be used to restrict the pathways seleted to those with matching evidence codes.

signature(object="ExpressionSet", idType="missing", setType="PfamCollection")

Construct a gene set collection by mapping all values in featureNames(object) to PfamIds found in the PFAM map implied by idType=AnnotationIdentifer(annotation(object)).

signature(object="ExpressionSet", idType="missing", setType="PrositeCollection")

Construct a gene set collection by mapping all values in featureNames(object) to ipi_id found in the PFAM map implied by idType=AnnotationIdentifer(annotation(object)).

signature(object="ExpressionSet", idType="missing", setType="ChrlocCollection")

Construct a gene set collection by mapping all values in featureNames(object) to chromosome, strand, and position information found in the CHRLOC map implied by idType=AnnotationIdentifer(annotation(object)).

signature(object="missing", idType="AnnotationIdentifier", setType="GOCollection")
signature(object="GOAllFrame", idType="missing", setType="GOCollection")

Construct a gene set collection containing all GO pathways referenced in the GOALLFrame provided. Each gene set only those Identifiers found in GOALLFrame. The ontology of each GOALLFrame GO ID will be included in the gene Set of that GO ID .

See Also

GeneSetCollection-class

Examples

gs1 <- GeneSet(setName="set1", setIdentifier="101")
gs2 <- GeneSet(setName="set2", setIdentifier="102")

## construct from indivdiual elements...
gsc <- GeneSetCollection(gs1, gs2)
## or from a list
gsc <- GeneSetCollection(list(gs1, gs2))

## set names must be unique
try(GeneSetCollection(gs1, gs1))

data(sample.ExpressionSet)
gsc <- GeneSetCollection(sample.ExpressionSet[200:250],
                         setType = GOCollection())

## Not run: 
## from KEGG identifiers, for example
library(KEGG.db)
lst <- head(as.list(KEGGEXTID2PATHID))
gsc <- GeneSetCollection(mapply(function(geneIds, keggId) {
    GeneSet(geneIds, geneIdType=EntrezIdentifier(),
            collectionType=KEGGCollection(keggId),
            setName=keggId)
}, lst, names(lst)))

## End(Not run)

Bioconductor/GSEABase documentation built on April 29, 2022, 12:04 p.m.