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.

Source Distribution

xlmhg-2.4.7.tar.gz (131.5 kB view hashes)

Uploaded Source

Built Distributions

xlmhg-2.4.7-cp36-cp36m-manylinux1_x86_64.whl (330.9 kB view hashes)

Uploaded CPython 3.6m

xlmhg-2.4.7-cp36-cp36m-manylinux1_i686.whl (306.8 kB view hashes)

Uploaded CPython 3.6m

xlmhg-2.4.7-cp36-cp36m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl (93.3 kB view hashes)

Uploaded CPython 3.6m macOS 10.10+ x86-64 macOS 10.6+ x86-64 macOS 10.9+ x86-64

xlmhg-2.4.7-cp35-cp35m-win_amd64.whl (81.8 kB view hashes)

Uploaded CPython 3.5m Windows x86-64

xlmhg-2.4.7-cp35-cp35m-win32.whl (70.0 kB view hashes)

Uploaded CPython 3.5m Windows x86

xlmhg-2.4.7-cp35-cp35m-manylinux1_x86_64.whl (328.3 kB view hashes)

Uploaded CPython 3.5m

xlmhg-2.4.7-cp35-cp35m-manylinux1_i686.whl (306.3 kB view hashes)

Uploaded CPython 3.5m

xlmhg-2.4.7-cp35-cp35m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl (93.1 kB view hashes)

Uploaded CPython 3.5m macOS 10.10+ x86-64 macOS 10.6+ x86-64 macOS 10.9+ x86-64

xlmhg-2.4.7-cp34-cp34m-manylinux1_x86_64.whl (340.1 kB view hashes)

Uploaded CPython 3.4m

xlmhg-2.4.7-cp34-cp34m-manylinux1_i686.whl (315.7 kB view hashes)

Uploaded CPython 3.4m

xlmhg-2.4.7-cp27-cp27mu-manylinux1_x86_64.whl (334.8 kB view hashes)

Uploaded CPython 2.7mu

xlmhg-2.4.7-cp27-cp27mu-manylinux1_i686.whl (312.3 kB view hashes)

Uploaded CPython 2.7mu

xlmhg-2.4.7-cp27-cp27m-win_amd64.whl (86.5 kB view hashes)

Uploaded CPython 2.7m Windows x86-64

xlmhg-2.4.7-cp27-cp27m-win32.whl (74.2 kB view hashes)

Uploaded CPython 2.7m Windows x86

xlmhg-2.4.7-cp27-cp27m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl (97.8 kB view hashes)

Uploaded CPython 2.7m macOS 10.10+ x86-64 macOS 10.6+ x86-64 macOS 10.9+ x86-64

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page