| GeneSetCollection-methods {GSEABase} | R Documentation |
Use GeneSetCollection to construct a collection of gene sets
from GeneSet arguments, or a list of
GeneSets.
GeneSetCollection(object, ..., idType, setType)
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. |
signature(object = "GeneSet",idType="missing", setType="missing")
GeneSet
arugments.
signature(object = "list", idType="missing", setType="missing")
GeneSets.
signature(object="missing", idType="AnnotationIdentifier", setType="CollectionType"),
signature(object="missing", idType="AnnotationIdentifier", setType="CollectionIdType")
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")
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")
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")
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")
idType. See the
signature(object="ExpressionSet", idType="missing",
setType="GOCollection") method for details.
GeneSetCollection-class
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)