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Command Line Script

The standalone command line script offers more flexibility in defining context values and background information. The current version of the script is available here.

Basic parameters

-x [filename]

Provide an input xgmml file (-x) for your network. Either this or -n is required. Example input files can be found on the script download page.

-n [filename]

Provide a list of gene IDs and context values for your network. Either this or -x is required. Example input files can be found on the script download page.

-a [attributeName]

Indicate the attribute name from your xgmml file that contains the context information.

-pV [pValue]

Indicate the pValue threshold for your context values. This will consider a value x to be contextual if 0 < x <= pValue. If no value is specified for either -pV or -fc, 0.1 is provided as the default. See also -fc, -aPV, -aFC.

-fc [foldChange]

Indicate the fold-change threshold for your context values. This will consider x to be contextual if foldChange <= x <= -foldChange. See also -aFC, -pV, -aPV.

-g [deGree threshold]

Indicate the number of interactors that defines a node as a hub. By default this is 5, but as biological networks can have nodes with hundreds of interactors you may want to adjust this higher based on the characteristics of your network.

-m [filename]

Provide a mitab file for background interaction data. This file is used to determine the "universe" of interactions that your network hubs will be compared to for the overrepresentation analysis. This is also used for network building. If no file is specified, one will be fetched from InnateDB. The script does assume an InnateDB formatted file, so if you have trouble with this option look at the example on the script download page.

-p [prefix]

Provide a prefix for your output. Files will be written to prefix-outputFileName.txt. If no value is provided, output will be written to outputFileName.txt. Files in your working directory with the same name will be overwritten without fanfare.

-v

This flag will print an additional file of output containing the values calculated for overrepresentation analysis in your network (number of connections, number of possible connections, number of nodes in the network, number of nodes in the universe).

Advanced parameters:

You may combine -pV and -fc, for instance if you want to consider a node contextual if it meets both fold-change and a p-value criteria. To do this, specify:

-aPV [attName1] -pV [pValue] -aFC [attName2] -fc [foldChange]

For greater flexibility in context specification, there is a custom range flag:

-r ["lowerBound...upperBound"]

-r "0...1" specifies the condition 0 < x < 1.

This can be combined with -l and -u to include the lower or upper bounds, respectively. So:

-r "0...0.1" -u specifies the condition 0 < x <= 0.1.

-r "5...15" -u -l specifies the condition 5 <= x <=15.

You may also vary whether the threshold values are included as contextual. For example, -pV 0.1 specifies the condition 0 < x <= 0.1. To include values of 0, use the range flag and add -l to include the lower bound.

-r "0...0.1" -u -l specifies the condition 0 <= x <= 0.1.

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The research leading to these results received funding from the European Union Seventh Framework Programme (FP7/2007-2013) PRIMES project grant FP7-HEALTH-2011-278568 & Science Foundation Ireland grant 09/IN.1/B2642.

Developed by the Lynn EMBL Australia Group.