SetRank (version 1.1.0)

exportMultipleResults: Export multiple SetRank networks and accompanying tables.

Description

Given a list of SetRank networks, writes out the following files for each network:

1. SetRank network in GML format called .gml where is the network name.
2. A TAB-delimited file listing the signficant pathways in the network, called _pathways.txt with the network name.
3. A TAB-delimited file listing which significant genes belong to which pathway, called _membership.txt with again the network name.

The network names will be taken from the names of the input list. Additionally, two global files will be created as well:

1. A Cytoscape VizMap visualisation file, calledsetrank.xml.
2. A TAB-delimited file listing which pathways are found in which networks, called "pathways.txt".

Usage

exportMultipleResults(networkList, selectedGenesList, collection, IDConverter = NULL, outputPath = "./")

Arguments

networkList

A named list of SetRank networks.

selectedGenesList

A named list with the same names as the networkList argument. Each list should be a vector with the set of significant genes as Entrez Gene IDs used to construct the SetRank network with the same name.

collection

The set collection used for the SetRank analysis.

IDConverter

Optional. By default, Entrez Gene IDs will be displayed in the output tables. This argument can be used to convert these into more human-friendly gene symbols. When supplied, should be a function that takes a vector of Entrez Gene IDs as single argument and returns the values of the corresponding gene symbols or whatever identifier you wish to have displayed in the output tables.

outputPath

The name of the directory where the results should be written. If the last element of the path doesn't exist, a directory will be created.

Value

None. Files are written out as a side effect.