xal {GSEABase}R Documentation

Read and Write XML Gene Sets

Description

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.

Usage

getBroadSets(uri, ...)
toBroadXML(geneSet, con, ...)
asBroadUri(name,
           base="http://www.broad.mit.edu/gsea/msigdb/cards")

Arguments

uri A file name or URL containing gene sets encoded following the Broad specification. Gene sets can be embedded in other elements, such as those for Broad's MSIGDB.
geneSet A GeneSet with collectionType BroadCollection (to ensure that required information is available).
con An optional 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.
... Further arguments passed to the underlying XML parser, particularly file used to specify an output connection for toBroadXML.

Value

getBroadSets returns a GeneSetCollection of gene sets.
toBroadXML returns a character vector of a single GeneSet or, if file is provided, writes the XML to a file.
asBroadUri can be used to create URI names (to be used by getBroadSets of Broad files.

Note

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.

Author(s)

Martin Morgan <mtmrogan@fhcrc.org>

References

http://www.broad.mit.edu/gsea/

See Also

GeneSetCollection GeneSet

Examples

## '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)

[Package GSEABase version 1.0.3 Index]