import.gsea.edb: Import a GSEA edb file. The edb file is a machine readable...
In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description Usage Arguments Details Value Note Author(s) References See Also Examples

These edb files are quite large, eg 22 MB for c2_all with 1000 permutations. Size is proportional to the number of permutations.

1	import.gsea.edb(x)

`x`	A GSEA directory.

The edb file is quite simple XML, utilising one node per geneset, and lots of attributes but not sub-terms for each geneset. We use the XML package, originally from Duncan Temple Lang.

The edb file in the form of an XMLDocument. See xmlTreeParse, This object appears to be immutable.

Here's some code I found useful in deciphering the XML document: edb.file <- "T47D_TreatedVsUntreated/c2_all.GseaPreranked.1236217933710/edb/results.edb" doc <- xmlTreeParse(edb.file) r <- xmlRoot(doc); xmlAttrs(r); xmlSize(r); xmlSize(r[[1]]) str(xmlAttrs(r[[1]])) xmlAttrs(r[[1]])[3] # modify the attributes... a <- xmlAttrs(r[[1]]) a[3] <- paste(a[3], "_MJC", sep="") n <- xmlNode("DTG", attrs=a) r[[1]] <- n

Mark Cowley, 2009-10-12

Omega hat XML: http://www.omegahat.org/RSXML/ Quick Guide to the XML package: http://www.omegahat.org/RSXML/Tour.pdf

xmlTreeParse, import.gsea, gsea.rename.genesets.edb

## Not run: 
edbT <- import.gsea.edb("T47D_TreatedVsUntreated/c2_all.GseaPreranked.1236217933710")
edbM <- import.gsea.edb("MCF7_TreatedVsUntreated/c2_all.GseaPreranked.1236217933720")
edb.merged <- merge.gsea.edb("T47D_TreatedVsUntreated/c2_all.GseaPreranked.1236217933710", "MCF7_TreatedVsUntreated/c2_all.GseaPreranked.1236217933720", c("T47D_", "MCF7_"), c("", ""))
export.gsea.edb(edb.merged, "./merged")

## End(Not run)