Framework for efficient high-dimensional association analyses. This is a fork of the original repository.

Navigate to directory where you want to install HASE and clone this repository: git clone https://github.com/roshchupkin/hase.git

1. Install the HDF5 software. The HDF5_DIR has to be added to the environment variables.

   export HDF5_DIR=~/hdf5<version-number>/hdf5/
   

2. HASE uses python version 2.7
3. To install the required packages, use pip install -r requirements.txt. Where requirements.txt is the file located within the root folder of this repository.

Use this wiki for the, original, upstream wiki. Or this wiki for a guide on using hase with the example data.

• Variants that do not have any variance across the samples are to be removed as this will cause an exception.
• Tests have made apparent that converting VCF and PLINK files not always result in correct HDF5 files. It is recommended to check this prior to proceeding analysis.

• Fixed bug causing an exception when more than 1000 individuals were used.
• Resolved bug causing the --intercept option having no effect.
• Made version numbers of pip packages explicit.
• Added commentary to code in places.

• Implemented the possibility for using interaction terms.
• Started implementing tests for both using, and not using interaction terms.

If you use HASE framework, please cite:

Roshchupkin, G. V. et al. HASE: Framework for efficient high-dimensional association analyses. Sci. Rep. 6, 36076; doi: 10.1038/srep36076 (2016)

This project is licensed under GNU GPL v3.

Gennady V. Roshchupkin (Department of Epidemiology, Radiology and Medical Informatics, Erasmus MC, Rotterdam, Netherlands)

Hieab H. Adams (Department of Epidemiology, Erasmus MC, Rotterdam, Netherlands)

If you have any questions/suggestions/comments or problems do not hesitate to contact us!

• g.roshchupkin@erasmusmc.nl
• h.adams@erasmusmc.nl