I am performing an exploratory analysis of the ENCODE Txn Factor ChiPseq data. For some reason that I cannot understand, the covplot function only works for certain input files. It works perfectly for certain input files but when I change just the input file and maintain the script the same I get the following error. All the files I want to analyze come from the ENCODE databse and are .narrowpeaks or .broadpeaks format. Then I transform them to a GRanges file to analyze them.
> covplot <- covplot(my_granges,weightCol ="score") #coverage plot Error in data.frame(chr = names(cov[i]), start = start(x), end = end(x), : arguments imply differing number of rows: 1, 118, 119
For example, when I use the ENCODE ChiPseq data for BCL11A in hESC.narrowpeaks or BCL11A in hESC Replicate 1.broadpeaks it works, but when I use BCL11A in hESC Replicate2.broadpeaks, it does not work.