Introduction

The 'BaseSpaceR' package provides a complete R interface to Illumina's BaseSpace REST API, enabling the fast development of data analysis and visualisation tools. Besides providing an easy to use set of methods for manipulating the data from BaseSpace, it also facilitate the access to R's rich environment of statistical and data analysis open source tools.

Features include:

  • Persistent connection with the REST server.
  • Support for the REST API query parameters.
  • Vectorized operations in line with the R semantic. Allows for queries across multiple Projects, Samples, AppResults, Files, etc.
  • S4 class system used to represent the BaseSpace data model.
  • Integration with Bioconductor libraries and data containers.
  • Templates for uploading and creating AppResults [under development].
  • Portability works on most platforms, Linux, Windows, Mac OS X.

We assume the user has some familiarity with the BaseSpace API and the R environment. It is essential for the developer to read through BaseSpace Getting Started guide before going forward with this document. Most of the exposed R methods take the same parameters as the REST methods they implement/use and we advise the developers to regularly check the REST API reference documentation.

The BaseSpaceR package is part of the Bioconductor repository. The package home page can be found here and contains basic installation instructions and documentation references.

Installation

This section briefly describe the necessary steps to get BaseSpaceR running on your system. We assume that the user have the R environment (see the R project at http://www.r-project.org) already installed and its familiar with it. BaseSpaceR requires R 2.15.0 or later and the following two packages, RCurl and RJSONIO, installed.

In order to install the package one needs first to install the core Bioconductor packages. If you have already installed Bioconductor packages on your system then you can skip the two lines below. Start R and enter at the prompt:

source("http://bioconductor.org/biocLite.R") biocLite()

Once the core Bioconductor packages are installed, BaseSpaceR can be installed by typing (first line can be ignored if already entered in the current session):

source("http://bioconductor.org/biocLite.R") biocLite("BaseSpaceR")

To use the package we load it using the library() function.

library(BaseSpaceR)

Note that when the package is loaded, both RCurl and RJSONIO packages are automatically loaded. Therefore the user doesn't need to explicitly load these two libraries if he intends to make use of their functionality.

Documentation and examples

Detailed documentation and illustration of various use cases can be found on the package homepage and the package vignette.

Feature Request and Bugs

Please feel free to report any feedback regarding the R SDK directly to the repository R SDK Repository, we appreciate any and all feedback about the SDKs. We will do anything we can to improve the SDK and make it easy for developers to use the SDK.