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?

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