GeneSetCollection-methods {GSEABase} | R Documentation

## Methods to construct GeneSetCollection instances

### Description

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

### 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 `GeneSet`s.

`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)

[Package GSEABase version 1.54.0 Index]