writeXGMML: Write Cytoscape input file

In CMPG/signet: signet: Selection Inference in Gene NETworks

Write Cytoscape input file

Description

This function allows to write an XGMML file to represent the results in Cytoscape.

Usage

writeXGMML(sigObj, filename = "signet_output.xgmml", threshold = 0.01)

Arguments

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.

Value

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.

Examples

# 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())

CMPG/signet documentation built on Jan. 31, 2024, 12:56 a.m.