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)