makeGOGraph(x, Ontology = "MF", removeRoot = TRUE, mapfun = NULL, chip = NULL)
mget(x, eg2gomap, ifnotfound=NA)
,
that is, NA
should be returned if a specified Entrez ID has
no GO mapping. See details for the interaction of mapfun
and
chip
.mapfun
.graph
class. The particular
implementation is not specified.
mapfun
is provided, it will be used to perform the
needed lookups. In this case, chip
will be ignored.
chip
is provided and mapfun=NULL
, then the
needed lookups will be done based on the Entrez to GO mappings
encapsulated in the specified annotation data package. This is
the recommended usage.
mapfun
and chip
are NULL
or missing,
then the function will attempt to load the GO package (the
environment-based package, distinct from GO.db). This package
contains a legacy environment mapping Entrez IDs to GO IDs. If
the GO package is not available, an error will be raised.
Omitting both mapfun
and chip
is not recommended as
it is not compatible with the DB-based annotation data packages.
The mappings are different for the different ontologies. Typically a GO indentifier is used only in one specific ontology.
The resulting structure is stored in a graph using the graph
package, again from Bioconductor.
oneGOGraph
library("hgu95av2.db")
set.seed(321)
gN <- unique(sample(keys(hgu95av2.db, 'ENTREZID'), 4))
gg1 <- makeGOGraph(gN, "BP", chip="hgu95av2.db")
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