I am trying to understand the output argument of ChIPpeakAnno annotatePeakInBatch(). According to the reference manual:
nearestLocation (default): will output the nearest features calculated as Peak- LocForDistance - FeatureLocForDistance;
shortestDistance: will output nearest features;
Those two options sound identical to me, but I realize they behave differently. I am also not sure why shortestDistance would generate multiple annotations per peak.