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SFUStatgen / LDheatmap

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Error when running LDheatmap.addGenes command #15

Open mariavictorxa opened 2 months ago

mariavictorxa commented 2 months ago

Hi,

I'm following the tutorial for LDheatmap and everything works great! However, when I attempt to annotate the LD plot by using the LDheatmap.addGenes command I get the following error:

Error in normArgTrack(track, trackids) : Unknown track: knownGene In addition: Warning message: In .local(x, ...) : 'track' parameter is deprecated now you go by the 'table' instead Use ucscTables(genome, track) to retrieve the list of tables for a track

mcneney commented 2 months ago

Hi, The warning message is from a function in the rtracklayer package. At this time we are unable to use rtracklayer in the LDheatmap.addGenes function. We hope to have a workaround at some point, but it has been slow going. Thanks for your interest in LDheatmap!