Installation

How to Install

GenEpi supports Python 3.7 and up. Use pip to install GenEpi and its dependencies.

$ pip install GenEpi

Check that you installed the GenEpi sucessfully.

$ GenEpi --help

After executed previous command on console, you will see:

usage: GenEpi [-h] -g G -p P [-s S] [-o O] [-m {c,r}] [-k K] [-t T]
              [--updatedb] [-b {hg19,hg38}] [--compressld] [-d D] [-r R]

optional arguments:
  -h, --help      show this help message and exit
  -g G            filename of the input .gen file
  -p P            filename of the input phenotype
  -s S            self-defined genome regions
  -o O            output file path
  -m {c,r}        choose model type: c for classification; r for regression
  -k K            k of k-fold cross validation
  -t T            number of threads

update UCSC database:
  --updatedb      enable this function
  -b {hg19,hg38}  human genome build

compress data by LD block:
  --compressld    enable this function
  -d D            threshold for compression: D prime
  -r R            threshold for compression: R square

Dependencies

Here is the dependency list for running GenEpi. pip takes care of these dependencies automatically when you install GenEpi.

• numpy >= 1.13.0
• psutil >= 4.3.0
• pymysql >= 0.8.0
• scipy >= 0.19.0
• scikit-learn == 0.21.2

System Requirements

For running a quick test, you could install GenEpi on any laptop e.g. a MacBook. When applying GenEpi on a real whole genome-wide dataset, here are recommended system requirements:

Processor:2.3 GHz Intel XEON® E5-2673 v4 * 32 RAM:256 GiB Storage:500 GiB

These requirements are refer to the specification of Microsoft Azure E32 v3.

Note

GenEpi is a memory-consuming package, which might cause memory errors when calculating the epistasis of a gene containing a large number of SNPs. We recommend that the memory for running GenEpi should be over 256 GB.