I have only recently come across ChIPQC, but I find it incredibly useful, especially in combination with Diffbind. Unfortunately, I can only use some its functionalities at the moment, as I keep encountering an error when I run the ChIPQCreport function:
sam = ChIPQC("DBsheet_SzabiChipSeq1.csv")
Error in `*tmp*` : object of type 'environment' is not subsettable
Calling traceback() reveals that the error occurs with plotRap(), which I next confirmed by attempting to run it separately, only to get the same error.
6: plotRap(object, facetBy = facetBy, addMetaData = addMetaData) 5: plotRap(object, facetBy = facetBy, addMetaData = addMetaData) 4: grid.draw(plot) 3: ggsave(plotRap(object, facetBy = facetBy, addMetaData = addMetaData), filename = file.path(reportFolder, "Rap.png")) 2: ChIPQCreport(sam) 1: ChIPQCreport(sam)
Interestingly, when I run either the function or the report with a single sample (i.e. with QCsample), everything works fine. Just to make sure that there are no conflicting samples, I tried with every one of them individually, and they all succeeded. The same happened when I took an entirely different dataset and I repeated my previous steps: the report of the experiment failed, but individual samples were ok.
Am I doing anything wrong? This is my sample sheet:
I am aware that we have no replicates, but that is something we are currently working on.
Thanks in advance,