Brad, Thanks for the feedback! Could you please send us the input files WT312, WT313? I assume that you are aware of the two parameters you can tune. maxgap Non-negative integer. Intervals with a separation of maxgap or less are considered to be overlapping, default 0 Minoverlap Non-negative integer. Intervals with an overlapping of minoverlap or more are considered to be overlapping, default to 1 For future correspondence, could you please keep the discussion in the bioconductor list so others can contribute or benefit? Thanks! Best regards, Julie On 8/13/14 12:55 PM, "Brad Davis" <bdavis at="" bcgsc.ca=""> wrote: > Hi Julie, > > I have a question about ChipPeaksAnno and how it calculates the size of an > intersection between two bed files. I have read in a few BED files that > contain the locations of histone mark enriched regions as follows: > > WT312 = > BED2RangedData(data.BED="A34082.H3K4me3.WT312.Thyroid.BED.sorted.col lapsed.1") > WT313 = > BED2RangedData(data.BED="A34089.H3K4me3.WT313.Thyroid-Adenoma- Follicular.BED.s > orted.collapsed.1") > WT340 = > BED2RangedData(data.BED="A34381.H3K4me3.WT340.Thyroid.BED.sorted.col lapsed.1") > WT341 = > BED2RangedData(data.BED="A34388.H3K4me3.WT341.Thyroid-Adenoma- Follicular.BED.s > orted.collapsed.1") > WT354 = > BED2RangedData(data.BED="A34707.H3K4me3.WT354.Thyroid.BED.sorted.col lapsed.1") > WT355 = > BED2RangedData(data.BED="A34714.H3K4me3.WT355.Thyroid- Goiter.BED.sorted.collap > sed.1") > > and then I use the makeVennDiagram package to actually display various > comparisons. for example WT312 vs WT313 > > makeVennDiagram(RangedDataList(WT312, WT313), NameOfPeaks=c("WT312", "WT313"), > totalTest=1000000, fill=brewer.pal(n=3, "Set1")[1:2], col=brewer.pal(n=3, > "Set1")[1:2]) > > However, the size of the overlapping region returned by ChipPeakAnno is > different than what I get from using > > bedops -i A34082.H3K4me3.WT312.Thyroid.BED.sorted.collapsed.1 > A34089.H3K4me3.WT313.Thyroid-Adenoma- Follicular.BED.sorted.collapsed.1 | wc -l > > or > > bedtools intersect -a A34082.H3K4me3.WT312.Thyroid.BED.sorted.collapsed.1 -b > A34089.H3K4me3.WT313.Thyroid-Adenoma- Follicular.BED.sorted.collapsed.1 | wc -l > > But I don't understand why that would be. I know I've seen a bit of a > discussion about this before, but I can't find it anywhere now. > > Do you have an explanation for this difference in behaviour? If I recall > correctly it has something to do with if a region in bed file A intersects > with multiple regions in bed file B, but I'm not certain. > > Thanks, > Brad >