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")
- 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="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="missing", idType="AnnotationIdentifier", setType="GOCollection")
- Construct a gene set collection containing all GO pathways
referenced in the annotation package of
idType
. See the
signature(object="ExpressionSet", idType="missing",
setType="GOCollection")
method for details.
See Also
GeneSetCollection
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())
[Package
GSEABase version 1.4.0
Index]