Import fusion inspector#22
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plijnzaad wants to merge 20 commits into
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leave this up to end user (e.g. MT-chr3 fusions display fine)
(cherry picked from commit f17c89decb83c2bc97811231b97f546672767d03)
(cherry picked from commit 8768ce180b2c7b324c980940e4457f7be0fa6835)
... but only if column PROT_FUSION_TYPE is available (i.e. when reading star-fusion.fusion_predictions.abridged.annotated.coding_effect.tsv ) If the (default) "star-fusion.fusion_predictions.abridged.tsv" file is used, inframe remains NA (and a warning is issued) now also setting fusion@inframe ...
... to make R CMD check shut up
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This PR implements the import of STAR-Fusion+FusionInspector output in order to get a
plotFusionReads-like plot. FusionInspector creates a virtual 'mini genome' to which the fusion reads are again aligned. Unfortunately, the chromosomes and coordinates are therefore completely different, soplotFusionReadsneeds some simplifications (functionplotFusionReadsSimple) to work, andplotCircle,plotFusionsandplotTranscriptsall fail, because of the different coordinate systems.It may still be useful to some people. E.g., I currently read the fusion data in in two ways: plain STAR-Fusion for
plotCircle,plotFusionsandplotTranscripts; and inuseFusionInspector=TRUEmode forplotFusionReadsSimple. (The latter is still really bare bones BTW)