Question

Is there an R package providing an R API for IGV / igvtools out there?

2

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Henrik Bengtsson ★ 2.4k

@henrik-bengtsson-4333

Last seen 18 months ago

United States

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?

package IGV • 3.4k views

ADD COMMENT • link updated 9.7 years ago by Paul Shannon ▴ 470 • written 9.7 years ago by Henrik Bengtsson ★ 2.4k

score 2 · Answer 1 · 2016-03-01

2

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Paul Shannon ▴ 470

@paul-shannon-5944

Last seen 3.5 years ago

United States

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 COMMENT • link 9.7 years ago Paul Shannon ▴ 470

0

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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 REPLY • link 9.7 years ago Henrik Bengtsson ★ 2.4k