opencgaR - R library

If you're a R user and you're keen of running OpenCGA through R, you're in the right place!

Overview

opencgaR is an R library that interacts with OpenCGA REST API to execute any operation supported by the web services through R code.

The client offers programmatic access to the implemented REST web services, facilitating the access and analysis of data stored in OpenCGA. From version 2.0.0 data is returned in a new RestResponse object which contains metadata and the results. The client also implements some handy methods to return information from this object.

opencgaR code has been implemented by Marta Bleda. It's open-source and can be found at https://github.com/opencb/opencga/tree/develop/opencga-client/src/main/R. It can be installed easily by downloading the pre-build package. Please, find more details on how to use the R library at Using the R client.

Installation

Requisites

• An operating machine with R installed and functional. opencgaR requires at least R version 3.4 (although most of the code is fully compatible with earlier versions).

• Have the pre-build R package stored in your local machine. Alternatively you can also provide the URL to the pre-build R package file.

  The pre-build R package of opencgaR can be downloaded from the OpenCGA v2.0.0 GitHub Release at https://github.com/opencb/opencga/releases.

Once requirements have been fulfilled, installing opencgaR becomes as easy as use the install.packages function in R. install.packages can also install a source package from a remote .tar.gz file by providing the URL to such file.

Installation from the R terminal

## Install opencgaR by providing the URL to the package
> install.packages("opencgaR_2.0.0.tar.gz", repos=NULL, type="source")