Description Usage Arguments Value
Given a list of SetRank networks, writes out the following files for each network:
SetRank network in GML format called <n>.gml
where <n>
is the network name.
A TAB-delimited file listing the signficant pathways in the network,
called <n>_pathways.txt
with <n>
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.
The network names will be taken from the names of the input list. Additionally, two global files will be created as well:
A Cytoscape VizMap visualisation file, calledsetrank.xml
.
A TAB-delimited file listing which pathways are found in which networks, called "pathways.txt".
1 2 | exportMultipleResults(networkList, selectedGenesList, collection,
IDConverter = NULL, outputPath = "./")
|
networkList |
A named list of SetRank networks. |
selectedGenesList |
A named list with the same names as the
|
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. |
None. Files are written out as a side effect.
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