compile.grn.from.kegg {EnrichmentBrowser} | R Documentation |
To perform network-based enrichment analysis a gene regulatory network (GRN) is required. There are well-studied processes and organisms for which comprehensive and well-annotated regulatory networks are available, e.g. the RegulonDB for E. coli and Yeastract for S. cerevisiae. However, in many cases such a network is missing. A first simple workaround is to compile a network from regulations in the KEGG database.
compile.grn.from.kegg( pwys, out.file = NULL )
pwys |
Either a list of |
out.file |
Optional output file the gene regulatory network will be written to. |
if(is.null(out.file)): the gene regulatory network; else: none, as the gene regulatory network is written to file
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
KEGGPathway-class
,
parseKGML
,
download.kegg.pathways
# (1) download human pathways # pwys <- download.kegg.pathways("hsa") # (2) compile gene regulatory network # grn <- compile.grn.from.kegg(pwys) pwys <- system.file("extdata/hsa_kegg_pwys.zip", package="EnrichmentBrowser") hsa.grn <- compile.grn.from.kegg(pwys)