I have done differential expression of the peaks from ATAC-seq data using DESeq2.
I have A vs B (Let us call this X), B vs C (Let us call this Y), and C vs D (Let us call this Z). I would like to compare X - (Y and Z) to get the unique peaks that are differentially expressed only in X.
I have the data in the following format
Peak_name Chr Start End Width
I tried something as simple as the function merge in R but not sure if it is the right way to do it. And I am not sure if the overlap functions in diffbind works for this. I tried
list1=merge(Y,Z, by.x = 0, by.y =0) list2=merge(X,list1, by.x=0, by.y=0)