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Provides a simple R script that transforms API query results into GAlignments.
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CONTRIBUTING.rst
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README.rst
genomics-api.R

README.rst

api-client-r

This R client fetches data from the Google Genomics API and turns it into a GAlignments object provided by the GenomicRanges package.

This GAlignments object is then plotted using ggbio - but it can also be integrated with any of the other R packages that supports GAlignments or GRanges.

Getting started

  • First you'll need to setup an R environment. We have currently only tested with R 3.0.3. There are known issues in R 3.0.2 and R 3.1.0.

  • Then you'll need a valid client ID and secret. Follow the authentication instructions, but instead of downloading the JSON file, you'll pass the Client ID and Client secret values into the setup function.

  • In an R interpreter:

    source("/path/to/genomics-tools/client-r/genomics-api.R")
    setup("<client ID>", "<client secret>")
    getReadData()
    plotAlignments() # Plot basic alignment and coverage data
    

setup only needs to be run once. After it has been called, getReadData can then be run repeatedly. It fetches data from the API and can be used to search over any set of reads. You can pull up a different sequence position by specifying additional arguments:

getReadData(chromosome="chr3", start="121458049", end="121459049")

Or, you can use the readsetId argument to query a different readset entirely:

getReadData(readsetId="<myreadset>")

Both reads and alignments are exported as global variables so that you can use other Bioconductor tools to modify the data as you wish.

Troubleshooting

If the sample code does not work with R 3.0.3, please check that your sessionInfo() matches our testing environment.

> sessionInfo()
R version 3.0.3 (2014-03-06)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] Rsamtools_1.14.3     Biostrings_2.30.1    ggbio_1.10.16
 [4] ggplot2_0.9.3.1      GenomicRanges_1.14.4 XVector_0.2.0
 [7] IRanges_1.20.7       BiocGenerics_0.8.0   BiocInstaller_1.12.1
[10] httr_0.3             rjson_0.2.13

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.24.0     Biobase_2.22.0           biomaRt_2.18.0
 [4] biovizBase_1.10.8        bitops_1.0-6             BSgenome_1.30.0
 [7] cluster_1.15.2           colorspace_1.2-4         DBI_0.2-7
[10] dichromat_2.0-0          digest_0.6.4             Formula_1.1-1
[13] GenomicFeatures_1.14.5   grid_3.0.3               gridExtra_0.9.1
[16] gtable_0.1.2             Hmisc_3.14-4             httpuv_1.3.0
[19] jsonlite_0.9.6           labeling_0.2             lattice_0.20-29
[22] latticeExtra_0.6-26      MASS_7.3-31              munsell_0.4.2
[25] plyr_1.8.1               proto_0.3-10             RColorBrewer_1.0-5
[28] Rcpp_0.11.1              RCurl_1.95-4.1           reshape2_1.2.2
[31] RSQLite_0.11.4           rtracklayer_1.22.7       scales_0.2.3
[34] splines_3.0.3            stats4_3.0.3             stringr_0.6.2
[37] survival_2.37-7          tcltk_3.0.3              tools_3.0.3
[40] VariantAnnotation_1.8.13 XML_3.95-0.2             zlibbioc_1.8.0

Project status

Goals

  • Provide an R library that hooks up the Genomics APIs to all of the other great existing R tools for biology. This library should be consumable by R developers.
  • In addition, for non-developers, provide many Read and Variant analysis samples that can easily be run on API data without requiring a lot of prior biology or cs knowledge.

Current status

This project is in active development - the current code is very minimal and a lot or work is left. See GitHub issues for more details.

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