Analysis of Composition of Microbiomes
ANCOM is a novel statistical test that accounts for OTU dependencies when calculating group signficance. This software makes use of accelerated matrix multiplication and permutation tests to allow for these statistical tests to complete within a reasonable amount of time.
This software requires the following dependencies
python=3
pandas
biom-format
numpy >= 1.7
scipy >= 0.13.0If pip installed, the following command can be run
pip install -r requirements.txtThen the following commands can be run to ANCOM
python setup.py build
python setup.py installTo make things easier, I recommend checking out virtualenv to mitigate the dependency issues.
After installing this software, I recommend running the unittests to make sure that everything is working. That can be done by going to the cloned directory, and running the following command
nosetests .ANCOM has been submitted to scikit-bio found here
To get started using the accelerated permutation tests run the following code
>>> from ancomP.stats.ancom import ancom
>>> import pandas as pd
>>> table = pd.DataFrame([[12, 11, 10, 10, 10, 10, 10],
... [9, 11, 12, 10, 10, 10, 10],
... [1, 11, 10, 11, 10, 5, 9],
... [2, 11, 10, 11, 10, 5, 9],
... [221, 210, 9, 10, 10, 10, 10],
... [220, 210, 9, 10, 10, 10, 10],
... [200, 220, 10, 10, 13, 10, 10],
... [230, 210, 14, 10, 10, 10, 10]],
... index=['s1','s2','s3','s4','s5','s6', 's7','s8'],
... columns=['b1','b2','b3','b4','b5','b6','b7'])
>>> grouping = pd.Series([0, 0, 0, 0, 1, 1, 1, 1],
... index=['s1','s2','s3','s4','s5','s6', 's7','s8'])
>>> results = ancom(table, grouping, significance_test='permutative-anova', permutations=100)
>>> results['reject']
b1 True
b2 True
b3 False
b4 False
b5 False
b6 False
b7 FalseSome more information about ANCOM can be found at this blog post