Package: icikt
DescriptionTheiciktpackage provides a Python tool to calculate an information-content-informed
Kendall Tau correlation coefficient between arrays, while also handling missing
values or values which need to be removed.Full API documentation, user guide, and tutorial can be found onreadthedocsInstallationTheiciktpackage runs under Python 3.4+. Usepipto install.
Starting with Python 3.4,pipis included by default.Install on Linux, Mac OS Xpython3-mpipinstalliciktInstall on Windowspy-3-mpipinstalliciktUpgrade on Linux, Mac OS Xpython3-mpipinstallicikt--upgradeUpgrade on Windowspy-3-mpipinstallicikt--upgradeGitHub Package installationMake sure you havegitinstalled:gitclonehttps://github.com/MoseleyBioinformaticsLab/pythonICIKendallTau.gitDependenciesiciktrequires the following Python libraries:numpyandscipyfor mathmatical calculations.docoptfor a command line interface.Cythonfor optimized performance.To install dependencies manually:pip3installnumpypip3installscipypip3installdocoptpip3installcythonBasic usageTo use theiciktpackage, input a 2d array with n columns each representing
an array of data for a variable. TheiciktArraywill return two n x n 2d arrays for correlations and p-values.
Each element will correspond to the result of a combination of two columns in the input array. iciktArray can also
be called from the command-line interface given the file path for the data along with several optional parameters(more in docs/tutorial).Running through command line :icikticiktArray/path/to/file.tsv--data-format=tsv--replace=NoneRunning through python script :importnumpyasnpimporticiktdataArray=np.genfromtxt('/path/to/file.tsv',delimiter="\t")# or with random valuesdataArray=numpy.random.randn(100,2)# running just 2 arrays with iciktcorr,pVal,tMax=icikt.icikt(dataArray[:,0],dataArray[:,1])# running all combinations with iciktArrayscaled,corrRaw,pVals,tauMax=icikt.iciktArray(dataArray)LicenseA modified Clear BSD LicenseCopyright (c) 2021, Praneeth S. Bhatt, Robert M. Flight, Hunter N.B. Moseley
All rights reserved.Redistribution and use in source and binary forms, with or without
modification, are permitted (subject to the limitations in the disclaimer
below) provided that the following conditions are met:Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.Redistributions in binary form must reproduce the above copyright notice,
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and/or other materials provided with the distribution.Neither the name of the copyright holder nor the names of its contributors may be used
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