importMSigDB.xml {gep2pep} | R Documentation |
Creates a GeneSetCollection
object using the XML
distribution of the MSigDB (see references). The returned object
can be passed to createRepository
.
importMSigDB.xml(fname)
fname |
Path to an XML file downloaded from MSigDB. |
This function now just calls getBroadSets(fname)
from the GSEABase
package. However, it is left for
backward compatibility and as an entry point to package
functionalities.
A CategorizedCollection object
http://software.broadinstitute.org/gsea/downloads.jsp
## Not run: ## To run this example, first obtain the MSigDB database in XML ## format (see ## http://software.broadinstitute.org/gsea/downloads.jsp). It is ## assumed that the database is locally available as the file ## "msigdb_v6.0.xml". db <- importMSigDB.xml("msigdb_v6.0.xml") ## The database is now in an acceptable format to create a local ## repository using createRepository ## End(Not run) ## A small excerpt from the MSigDB is included in gep2pep. The ## following creates (and then deletes) a gep2pep repository. db_sample <- loadSamplePWS() db_sample <- as.CategorizedCollection(db_sample) repo_path <- file.path(tempdir(), "gep2pepTemp") rp <- createRepository(repo_path, db_sample) ## removing temporary repository unlink(repo_path, TRUE)