Dear kinga, Thanks for your kind word and great question! For peaks partially upstream and partially overlap with start, the $insideFeature will be assigned overlapStart. Here is the hierarchy of assignment. Inside, overlapEnd/overlapStart, includeFeature, upstream/downstream. Best regards, Julie On 11/14/12 11:50 AM, "Kinga Kamieniarz-Gdula" <kinga.kamieniarz- gdula@path.ox.ac.uk=""> wrote: Dear Julie, I am currently starting to use you package ChIPpeakAnno and am very happy with it, many thanks! What is not clear to me is how the function annotatePeakInBatch deals with peaks that eg. are partially upstream and partially overlaping with start. In other words belong to more than one category. How is the choice for value for $insideFeature made? Is there a hierarchy or is only one bp (middle, start) used for the annotation to a feature? I will be very grateful for helping me out! All the best, Kinga ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Kinga Kamieniarz-Gdula, PhD Proudfoot lab Sir William Dunn School of Pathology University of Oxford South Parks Road, Oxford, OX1 3RE, UK Tel: +44 01865 275568 [[alternative HTML version deleted]]