Installation¶
Running R code from CLARITE¶
In order to use the ewas_r function, it is recommended to install CLARITE using Conda:
Create and activate a conda environment with python 3.6 or 3.7:
$ conda create -n clarite python=3.7 $ conda activate clarite
Install rpy2 and related dependencies (optional). CLARITE has a version of the EWAS function that calls R code using the survey library:
$ conda install -c conda-forge rpy2 $ conda install r-essentials $ conda install r-survey
Install CLARITE:
$ pip install clarite
Install required R packages (such as survey) (optional):
$ clarite-cli utils install-r-packages