| getAnnMap {annotate} | R Documentation |
This function retrieves a map object from an annotation data package. It is intended to serve as a common interface for obtaining map objects from both SQLite-based and environment-based annotation data packages.
getAnnMap(map, chip, load = TRUE, type = c("env", "db"))
map |
a string specifying the name of the map to retrieve. For
example, "ENTREZID" or "GO" |
chip |
a string describing the chip or genome |
load |
a logical value. When TRUE, getAnnMap
will try to load the annotation data package if it is not
already attached. |
type |
a character vector of one or more annotation data
package types. The currently supported types are "db"
and "env". If load is TRUE, you can specify both "db"
and "env" and the order will determine which type is
tried first. This provides a fall-back mechanism when the
preferred annotation data package type is not available. If
type is missing, then the first matching annotation
package found in the search path will be used. |
getAnnMap expects the annotation data package to be loaded
and attached. If load is TRUE, the package will be attached.
If type is "db", an S4 object representing the
requested map. If type is "env", an R
environment object representing the requested map.
SQLite-based annotation data packages are planned for the BioC 2.1
release. Use of type="db" may not work as desired in this
release. In the next release, the order of "env" and
"db" will be reversed to give preference to the SQLite-based
packages.
Seth Falcon
map <- getAnnMap("ENTREZID", "hgu95av2")
class(map)