After ATAC-Seq analysis, I have a list of peaks
Now, I would like to merge our open regions from all samples into a set of non-redundant (no overlapping regions) open regions present in any sample (see example below).
I tried the following using soGGi
myPeaks <- lapply(peaks, ChIPQC:::GetGRanges, simple = TRUE) names(myPeaks) <- c("HindBrain_1", "HindBrain_2", "Kidney_1", "Kidney_2", "Liver_1", "Liver_2") Group <- factor(c("HindBrain", "HindBrain", "Kidney", "Kidney", "Liver", "Liver")) consensusToCount <- soGGi:::runConsensusRegions(GRangesList(myPeaks), "none")
But I always get a NULL when I do this. What would be the alternate to soGGI to unlist the peaks to get a consensus count of non-redundant peaks and add that as a metadata like in example above? Thanks.