Ron, If you assume 10% total histone are available for modification, then you would set totalTest = 3 * 10^9 bp / 146 * 0.1 which is about 2 million. For your new question, here is some code snippet that might address your needs. t1 =findOverlappingPeaks(peaks1, peaks2, maxgap=0, NameOfPeaks1="TF", NameOfPeaks2="Histone", select="First") AllPeaks = c(peaks1[!rownames(peaks1) %in% rownames(t1$Peaks1withOverlap),], peaks2[!rownames(peaks2) %in% rownames(t1$Peaks2withOverlap),], t1$MergedPeaks) Totals = rownames(AllPeaks) Sample.n = dim(t1$MergedPeaks)[1] ##### put the following code snippets in a loop allow you to sample from the total peak population multiple times s1 = AllPeaks[rownames(AllPeaks) %in% sample(Totals, Sample.n),] go.s1 = getEnrichedGO(annotatePeakInBatch(s1,....), ....) ################## Please let me know if you come up with more elegant ways to do this. Thanks! Best regards, Julie On 3/14/12 5:35 PM, "Ron Hart" <rhart at="" rci.rutgers.edu=""> wrote: > Julie, > > In response to my last question and your phone call, I tried several values of > totalTest based on the recommendations but I could only get either a 0 or a 1 > value. For histone marks, I used as the largest estimate the total number of > possible histone overlaps (3 x 10^9 bp / 146 bp per nucleosome). Then I tried > the sum of the two sets of marks, but nothing made sense for me. So I gave > up trying to get a p-value. It?s really not important for my study. > > New question. I?m using the overlap function to extract intersecting peaks in > common between two marks. Everything is working great. But I?d like to > compare the result to a random sampling of the same number of peaks from the > union set of both marks. I think this sort of a bootstrapping approach would > be convincing that my enriched GO list was unique to the actual intersection > of the two sets of peaks. > > Ideally, I?d like to merge two annotated peak objects and then sample them for > the number I observed in the intersection set (which I know). Since I?m not > that familiar with working with IRanges-based objects, can you suggest a code > snippet that would work for me? > > Does that make sense? > > Ron >