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
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?