GeneSetCollection
to construct a collection of gene sets
from GeneSet
arguments, or a list of
GeneSet
s.
GeneSetCollection(object, ..., idType, setType)
GeneIdentifierType
, used to
indicate how the geneIds
will be represented.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")
GeneSet
s.
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")
signature(object="character", idType="AnnotationIdentifier",
setType="GOCollection")
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")
object
to PfamIds
found in the PFAM
map
implied by idType
. signature(object="character", idType="AnnotationIdentifier",
setType="PrositeCollection")
object
to ipi_ids
found in the PFAM
map
implied by idType
. signature(object="character", idType="AnnotationIdentifier",
setType="ChrlocCollection")
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")
featureNames(object)
to PfamIds
found in the
PFAM
map implied by idType=AnnotationIdentifer(annotation(object))
. signature(object="ExpressionSet", idType="missing", setType="PrositeCollection")
featureNames(object)
to ipi_id
found in the
PFAM
map implied by idType=AnnotationIdentifer(annotation(object))
. signature(object="ExpressionSet", idType="missing", setType="ChrlocCollection")
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")
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 .
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)
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