GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment

[kyliuae]

Hi,

I just want to see if anyone have bump into this problem before but i recently try to use the code from the ChIPseq tutorial in Part 4 but it seems not working as when i work on this step:

allPeaksSet_nR_H3K4me1 <- reduce(allPeaksSet_Overlapping_H3K4me1)
allPeaksSet_nR_H3K4me1

The step doesn't work anymore. I attach a screenshot below as reference. I think the allPeaksSet_nR file should be correct, so i really have no idea what is the problem.

Thank you very much for the help.

[matthew-paul-2006]

Hi there,

So it seems you are using a different dataset to the one we provided so it is hard to determine the exact issue. I have rerun this section of code on my end and it looks ok.

My first guess is that you may have another package installed that has a function called reduce. Could you try running the command below. This will directly specify that we want to use the GenomicRanges reduce function.

allPeakSet_nR_H3K4me1 <- GenomicRanges::reduce(allPeaksSet_Overlapping_H3K4me1)

If that does not work I need a little more information about your set up.

Could your run the sessionInfo() command. Then paste the response back here so I can see what package versions you are working with. Maybe something has changed.

[kyliuae]

Hi Paul,

I find the problem. The GenomicRanges::reduce does work.

Thank you for the prompt and detailed explanation and help for my careless mistake.

[matthew-paul-2006]

Great news. No problem at all. This is a common mistake. One I've made countless times.