GoogleGenomics |Build Status|_

.. |Build Status| image:: http://img.shields.io/travis/Bioconductor/GoogleGenomics.svg?style=flat .. _Build Status: https://travis-ci.org/Bioconductor/GoogleGenomics

.. role:: r(code) :language: r

.. role:: sh(code) :language: sh

This R client fetches reads and variants data from the Google Genomics API_ and provides converters to obtain Bioconductor_ S4 classes like GAlignments, and GRanges and VRanges.

.. _Google Genomics API: https://cloud.google.com/genomics .. _Bioconductor: http://www.bioconductor.org/ .. _gRPC: https://grpc.io/

Installing

Use the Bioconductor repositories to install this package.

If you have gRPC_ installed, you will be able to access the entire v1 Google Genomics API through the :r:callGRPCMethod function provided in the package and use more performant reads and variant search methods. Without gRPC support, you will still be able to query reads and variants; see the vignettes for sample usage.

• [Optional] Installing gRPC

  See our guide on gRPC <GRPC.rst>_.

• Installing R package

  .. code:: r

  source("http://bioconductor.org/biocLite.R") useDevel(TRUE) # Skip this step if you do not want the devel version.

  biocLite("GoogleGenomics") # If gRPC is not installed. biocLite("GoogleGenomics", type="source") # If gRPC is installed. library(GoogleGenomics)

Authentication

Call :r:authenticate to set up credentials. Check the function documentation for details on various available options. The function will return :r:TRUE on successful authentication.

Examples

See the following examples for more detail:

• Working with Reads <http://bioconductor.org/packages/devel/bioc/vignettes/GoogleGenomics/inst/doc/PlottingAlignments.html>_

• Working with Variants <http://bioconductor.org/packages/devel/bioc/vignettes/GoogleGenomics/inst/doc/AnnotatingVariants.html>_

• Variant Annotation Comparison Test <http://bioconductor.org/packages/devel/bioc/vignettes/GoogleGenomics/inst/doc/VariantAnnotation-comparison-test.html>_

• and also the integration tests <./tests/testthat>_

Project status

The package is integrated with gRPC when available on the system where the package was built. With gRPC support, the entire v1 API is accessible. Without gRPC support, this package can be used to search for reads and variants, and convert them to various Bioconductor formats.