import/export {GSEABase} | R Documentation |
getBroadSets
parses one or more XML files for gene sets. The
file can reside locally or at a URL. The format followed is that
defined by the Broad (below). toBroadXML
creates Broad XML
from BroadCollection
gene sets.
toGmt
converts GeneSetColletion
objects to a character
vector representing the gene set collection in GMT
format. fromGmt
reads a file or other character vector into a
GeneSetColletion
.
getBroadSets(uri, ...) toBroadXML(geneSet, con, ...) asBroadUri(name, base="http://www.broad.mit.edu/gsea/msigdb/cards") getGmt(con, geneIdType=NullIdentifier(), collectionType=NullCollection(), sep="\t", ...) toGmt(x, con, ...)
uri |
A file name or URL containing gene sets encoded following the Broad specification. For Broad sets, the uri can point to a MSIGDB. |
geneSet |
A GeneSet with
collectionType BroadCollection (to ensure that
required information is available). |
x |
A GeneSetCollection or other object for
which a toGmt method is defined. |
con |
A (optional, in the case of toXxx ) file name or
connection to receive output. |
name |
A character vector of Broad gene set names, e.g.,
c('chr16q', 'GNF2_TNFSF10') . |
base |
Base uri for finding Broad gene sets. |
geneIdType |
A constructor for the type of identifier the members
of the gene sets represent. See GeneIdentifierType for
more information. |
collectionType |
A constructor for the type of collection for the
gene sets. See CollectionType for more information. |
sep |
The character string separating members of each gene set in the GMT file. |
... |
Further arguments passed to the underlying XML parser,
particularly file used to specify an output connection
for toBroadXML . |
getBroadSets
returns a GeneSetCollection
of gene sets.
toBroadXML
returns a character vector of a single
GeneSet
or, if con
is provided, writes the XML to a
file.
asBroadUri
can be used to create URI names (to be used by
getBroadSets
of Broad files.
getGmt
returns a GeneSetCollection
of gene sets.
toGmt
returns character vectors where each line represents a
gene set. If con
is provided, the result is written to the
specified connection.
Actual Broad XML files differ from the DTD (e.g., an implied ',' separator between genes in a set); we parse to and from files as they exists the actual files.
Martin Morgan <mtmrogan@fhcrc.org>
http://www.broad.mit.edu/gsea/
## 'fl' could also be a URI fl <- system.file("extdata", "Broad.xml", package="GSEABase") gss <- getBroadSets(fl) # GeneSetCollection of 2 sets names(gss) gss[[1]] ## Not run: ## Download from the Broad getBroadSets(asBroadUri(c('chr16q', 'GNF2_ZAP70'))) ## End(Not run) fl <- tempfile() toBroadXML(gss[[1]], con=fl) noquote(readLines(fl)) unlink(fl) ## Not run: toBroadXML(gss[[1]]) # character vector ## End(Not run) fl <- tempfile() toGmt(gss, fl) getGmt(fl) unlink(fl)