Description Usage Arguments Value Author(s)
Given a single SetRank analysis result, writes out the following files:
SetRank network in GML format called <n>.gml
where <n>
is the specified network name.
A Cytoscape VizMap visualisation file, called setrank.xml
.
A TAB-delimited file listing the signficant pathways in the network,
called <n>_pathways.txt
with <n>
again the network name.
A TAB-delimited file listing which significant genes belong to which
pathway, called <n>_membership.txt
with <n>
again the network
name.
1 2 | exportSingleResult(network, selectedGenes, collection, networkName,
IDConverter = NULL, outputPath = "./")
|
network |
A SetRank network. |
selectedGenes |
A vector with the set of significant genes as Entrez
Gene IDs. This should be the same set passed to the
|
collection |
The set collection used for the SetRank analysis. |
networkName |
A name used to name the different output files. |
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. |
None. Files are written out as a side effect. genes = sprintf("gene_ geneSets = lapply(1:9, function(i) sample(genes[((i-1)*10):((i+1)*10)], 10)) annotationTable = data.frame(termID=sprintf("set_ geneID=unlist(geneSets), termName = sprintf("dummy gene set dbName = "dummyyDB", description = "A dummy gene set DB for testing purposes") collection = buildSetCollection(annotationTable, referenceSet=genes) network = setRankAnalysis(genes, collection, TRUE) exportSingleResult(network, genes, collection, "example", function(x) x, "example_dir")
Cedric Simillion
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