[BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation

Julian Gehring julian.gehring at embl.de
Wed Dec 11 11:03:57 CET 2013

Hi Thomas,

I agree with you that there is obviously no right or wrong on how to 
report the effect of variants - different solutions have their pros and 

> results up in the complete variant report. Alternatively, one could
> easily do the same on the transcript level, but here a summary report
> may become quickly too complex to be useful for practitioners. Perhaps a
> well designed Var Summary Report function would include a summary_mode
> argument where the user could decide whether to output a gene- or
> transcript-centric summary_var_report.

One could generalize it even more, e.g. for summarizing over affected 
proteins or any desired variable of interest.  If I understood you 
correctly, one would need to pass the respective column name to the 
'tapply' function.

Best wishes

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