scikit-mdr
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EpistasisLab
A sklearn-compatible Python implementation of Multifactor Dimensionality Reduction (MDR) for feature construction.
genetic_data = pd.read_csv('https://github.com/EpistasisLab/scikit-mdr/blob/master/data/GAMETES_Epistasis_2-Way_20atts_0.4H_EDM-1_1.tsv.gz', sep='\t', compression='gzip') The above command is not working, error says : "BadGzipFile: Not a gzipped file (b'\n\n')"
https://github.com/EpistasisLab/scikit-mdr/blob/master/mdr/mdr.py#L126 is throwing DeprecationWarning: `np.int ` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and...
Hi, What code should I use to output the cross-validation consistency and prediction error for each 2-way models I had generated? Thank you, Jennifer
It seems that the utilities in `mdr.utils` is designed for this purpose but there is no documentation about how to use them. I have a quick look into those codes...
I tried to install scikit-mdr on an Ubuntu 14.04 Linux via pip install but got this error below. To make sure it wasn't a versions issue with scikit-learn, I did...
Hi, I have a ChIP-seq style dataset of RPKM values that I want to reduce from 200x200000 into 200x1000, so that I only end up with 1000 variables at the...
Instead of keeping all of the modules in the same `utils.py` file, break them out into separate submodules. This will help prevent situations where, for example, a user imports matplotlib...
Provide common functions for MDR such as: - [x] Entropy / MDR entropy measures - Common MDR visualizations - [x] Colorized MDR grid - [ ] Entropy network - [x]...
A reminder to add a warning to make sure that encodings (both phenotype and genotype) are consistent when working with a discovery and a replication dataset.
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A sklearn-compatible Python implementation of Multifactor Dimensionality Reduction (MDR) for feature construction.