writeXGMML: Write Cytoscape input file

Description Usage Arguments Value Examples

View source: R/writeXGMML.R

Description

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

Usage

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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

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# 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 Dec. 12, 2017, 11:05 a.m.