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.
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.
BaseSpaceR package is part of the Bioconductor repository. The package home page can be found here and contains basic installation instructions and documentation references.
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,
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:
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):
To use the package we load it using the
Note that when the package is loaded, both
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.
Detailed documentation and illustration of various use cases can be found on the package homepage and the package vignette.
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.