writeXGMML {signet} | R Documentation |
This function allows to write an XGMML file to represent the results in Cytoscape.
writeXGMML(sigObj, filename = "signet_output.xgmml", threshold = 0.01)
sigObj |
A signet or signetList object. |
filename |
The desired file name. Default is "signet_output.xgmml". |
threshold |
Significance threshold (default: 0.01). If a signetList is provided, all subnetworks with a p-value below this threshold will be merged and represented. |
Writes an XGMML file in the working directory. If a single pathway (signet object) is provided, the whole pathway is represented and nodes belonging to the highest-scoring subnetwork (HSS) are highlighted in red. If a list of pathways (signetList) is provided, all subnetworks with a p-value below a given threshold (default: 0.01) are merged and represented. Note that in this case, only the nodes belonging to HSS are kept for representation.
# Get KEGG pathways from the package graphite: # library(graphite) # kegg <- pathways("hsapiens", "kegg") # kegg_human <- lapply(kegg, pathwayGraph) data(daub13) # load the gene scores from Daub et al. (2013) #run the search in all the pathways with 2500 iterations (default) example <- searchSubnet(kegg_human, scores) #write Cytoscape input file for the first pathway: writeXGMML(example[[1]], filename = tempfile())