[BioC] summarizeOverlaps: number of dropped reads

[Gabriele Schweikert]

Hello,

I'm using summarizeOverlaps with mode=union and inter.feature=TRUE to  
count reads that overlap annotated features. This is great and exactly  
what I need. However, I would also like to know how many reads are  
dropped in this setting because they map to multiple features (as  
opposed to reads not mapping to any of the annotated features.) Is  
there an easy way to get this number?
I was thinking of counting again, this time with inter.feature=FALSE  
and subtracting the results, but this is not quite what I want because  
multiple reads are then also counted multiple times.

Thanks for the assistance

best wishes

Gabriele




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