Description Usage Arguments Details Value References Examples
Creates a GeneSetCollection
object using the XML
distribution of the MSigDB (see references). The returned object
can be passed to createRepository
.
1 | importMSigDB.xml(fname, organism = "Homo Sapiens")
|
fname |
Path to an XML file downloaded from MSigDB. |
organism |
Select only gene sets for a given organism. Default is "Homo Sapiens". |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ## 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()
repo_path <- file.path(tempdir(), "gep2pepTemp")
rp <- createRepository(repo_path, db_sample)
## removing temporary repository
unlink(repo_path, TRUE)
|
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