igvShiny issues with loading local bams
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7 weeks ago
genya35 ▴ 40

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

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why not use IGV browser directly?

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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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7 weeks ago
Malcolm.Cook ★ 1.5k

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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