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consensusClustersGR() row.names problem #112
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Hello, I do not understand how you manage to run the Best, Charles |
Hi, Can you please specify what the 3rd argument should be please? Or maybe if there is a different function for this that I am missing? |
I am sorry, I got confused with |
Hello,
I have a problem that didn't occur before while using only 3 data stages. But now that I added a 4th data set there is a problem.
First I did:
After that, I created a consensus ranges:
This worked no problem but when I want to annotate this set of consensus clusters using ChIPseeker or even convert it to a data frame I get this error:
It stops roughly after half of the data is annotated (39k/62k).
I have looked into it and apparently, the row.names that it has a problem with are in the elementMetadata. But even though I tried setting specific row.names for the metadata it still gives me the same error and I don't see N.4DAG.1, D4.A, N.4DAG.2, D8.Others, D8.No5, D4.B, D24.B, D24.A in any place in the structure. (the names are the BAM file names and I did not merge replicates since I use the data for deseq analysis)
For now, I have fixed it by deleting the metadata and annotating it without it, since I don't need the metadata for the current task but I would like to know if this is a CAGEr error or possibly some mistake on my part.
Thank you.
Here is my session info:
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