Skip to main content

XL-mHG: A Semiparametric Test for Enrichment

Project description

PyPI version Python versions supported License
master Coverage (master branch) Travis-CI build Status (master branch) Appveyor build Status (master branch) Documentation Status (master branch)
develop Coverage (develop branch) Travis-CI build Status (develop branch) Appveyor build Status (develop branch) Documentation Status (develop branch)

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.

Installation

$ pip install xlmhg

Getting started

The 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 statistic
  • cutoff: The cutoff at which XL-mHG test statistic was attained
  • pval: The XL-mHG p-value

Documentation

Please refer to the XL-mHG User Manual (hosted on ReadTheDocs).

Citing XL-mHG

If you use the XL-mHG test in your research, please cite Eden et al. (PLoS Comput Biol, 2007) and Wagner (PLoS One, 2015).

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for xlmhg, version 2.4.9
Filename, size File type Python version Upload date Hashes
Filename, size xlmhg-2.4.9-cp27-cp27m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl (98.1 kB) File type Wheel Python version cp27 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp27-cp27mu-manylinux1_i686.whl (313.6 kB) File type Wheel Python version cp27 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp27-cp27mu-manylinux1_x86_64.whl (334.3 kB) File type Wheel Python version cp27 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp27-cp27m-win32.whl (74.5 kB) File type Wheel Python version cp27 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp27-cp27m-win_amd64.whl (86.7 kB) File type Wheel Python version cp27 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp34-cp34m-manylinux1_i686.whl (315.2 kB) File type Wheel Python version cp34 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp34-cp34m-manylinux1_x86_64.whl (340.9 kB) File type Wheel Python version cp34 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp35-cp35m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl (93.4 kB) File type Wheel Python version cp35 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp35-cp35m-manylinux1_i686.whl (306.7 kB) File type Wheel Python version cp35 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp35-cp35m-manylinux1_x86_64.whl (328.8 kB) File type Wheel Python version cp35 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp35-cp35m-win32.whl (70.3 kB) File type Wheel Python version cp35 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp35-cp35m-win_amd64.whl (82.0 kB) File type Wheel Python version cp35 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp36-cp36m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl (93.6 kB) File type Wheel Python version cp36 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp36-cp36m-manylinux1_i686.whl (307.2 kB) File type Wheel Python version cp36 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9-cp36-cp36m-manylinux1_x86_64.whl (331.2 kB) File type Wheel Python version cp36 Upload date Hashes View hashes
Filename, size xlmhg-2.4.9.tar.gz (131.8 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page