ME-Class2

Installation

Using pip:

download meclass2-0.2.0.tar.gz
pip install meclass2-0.2.0.tar.gz

For a user-specific install use --user flag:

pip install --user meclass2-0.2.0.tar.gz

Required packages

• sklearn >= 0.18
• numpy
• scipy
• seaborn
• matplotlib
• pandas

We recommend installing anaconda or a similar all in one scientific package which will include all of these.

Quick start using example data

1) Setup example_data

download example_data.tgz
tar -xzf example_data.tgz
cd example_data

2) Run interpolation

meclass2_interpolation --autosome-only -g refGene_sample.txt -z sample_data_5hmC.bg sample_data_5mC.bg sample_data.expr HRPS_test HRPS

Example run time: ~20-30 minutes

3) Run Classifier

meclass2_classifier --num_trees 1001 -t 5hmC .
meclass2_classifier --num_trees 1001 -t 5mC .
meclass2_classifier --num_trees 1001 -t 5mC_5hmC .

Example run time: ~3-5 minutes each or faster if using multiple threads (-j option)

4) Report Results

meclass2_reporting --plot_results *.pred

Example run time: <1 minute

5) Run clustering

meclass2_clustering . cluster --tag 5mC_5hmC --numClusters=4 --lowerPredBound=0.75

Example run time: ~1 minute

Known Issues

1. There is a warning thrown in the clustering script about a depreciated function (axisbg). This can be safely ignored.