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igvShiny issues with loading local bams

Hello, Has anyone here have tried IGV imbedded in Rshiny from https://github.com/gladkia/igvShiny? It installed ok but I can't get local bams from local path to load. It reads them but gives me an error: Error in as.character: cannot coerce type 'closure' to vector of type 'character' and does not display the track. I can't get to work with a local example bam they provided either.

Also, looks like the guy who made it has recently retired, therefore, not sure if my Github issues will be answered. Thanks

r igv shiny
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updated by Malcolm.Cook Malcolm.Cook • written by genya35 • genya35

IGV imbedded in Rshiny

I think they want to embed it in a Shiny app, and this package takes care of wrapping IGV.js up to play nicely.

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written by jared.andrews07 jared.andrews07

We need your code to have any chance of answering this.

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written by jared.andrews07 jared.andrews07

1 answer

I coded up a workaround for a very similar issue that I expect will apply to this case as well. See it here: loadBedGraphTrackFromURL rewrites the config vars including url

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written by Malcolm.Cook Malcolm.Cook

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