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Question: Is there an R package providing an R API for IGV / igvtools out there?
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gravatar for Henrik Bengtsson
21 months ago by
United States
Henrik Bengtsson2.4k wrote:

Does anyone know of an R package (on CRAN, Bioconductor, GitHub or elsewhere) that provides an R API to igvtools? It's quite easy to use an existing igvtools.jar built and distributed by the Broad Institute, e.g.

> library("rJava")
> .jinit(classpath="igvtool.jar")
> TDFUtils <- .jnew("org/broad/igv/tdf/TDFUtils")
> TDFUtils$tdfToBedgraph("GSM1824797_bt142_idm_ctcf_1.tdf", "GSM1824797_bt142_idm_ctcf_1.bed")

One could even imagine building the R API using Java reflection via rJava::.jmethods().

However, it would be neat if this is already wrapped up in an R package for easy installation.  Does anyone know if such an effort has already been undertaken?

 

 

ADD COMMENTlink modified 21 months ago by Paul Shannon360 • written 21 months ago by Henrik Bengtsson2.4k
2
gravatar for Paul Shannon
21 months ago by
Paul Shannon360
Paul Shannon360 wrote:

Hi Henrik,

With support from Jim Robinson (IGV developer), and starter code heisted from Sean's sradb package, I've just made a start on igvR:

https://github.com/paul-shannon/igvR

I hope to get this into the next bioc release.  Jim offered to add new features.  It would be great to get your comments, critique and suggestions.

 - Paul

ADD COMMENTlink written 21 months ago by Paul Shannon360

Thanks Paul, this looks promising.  I should have been a bit more clear in my question.  I'm looking for an access that does not require a separate installation of IGV.  In your case you seem to connect to a running instance of IGV via sockets.  I'm basically looking for a direct access to the Java Archive igvtools.jar (or igv.jar) and ideally someone is already distributing that as an R package.

ADD REPLYlink written 21 months ago by Henrik Bengtsson2.4k
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