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This is an efficient Python/Cython implementation of the semiparametric XL-mHG test for enrichment in ranked lists. The XL-mHG test is an extension of the nonparametric mHG test, which was developed by Dr. Zohar Yakhini and colleagues.
$ pip install xlmhgThe xlmhg package provides two functions (one simple and more more advanced) for performing XL-mHG tests. These functions are documented in the User Manual. Here's a quick example using the "simple" test function:
import xlmhg
stat, cutoff, pval = xlmhg.xlmhg_test(v, X, L)Where: v is the ranked list of 0's and 1's, represented by a NumPy array of
integers, X and L are the XL-mHG parameters, and the return values have
the following meanings:
stat: The XL-mHG test statisticcutoff: The cutoff at which XL-mHG test statistic was attainedpval: The XL-mHG p-value
Please refer to the XL-mHG User Manual (hosted on ReadTheDocs).
If you use the XL-mHG test in your research, please cite Eden et al. (PLoS Comput Biol, 2007) and Wagner (PLoS One, 2015).
Copyright (c) 2015-2019 Florian Wagner
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