Error in .local(x, na.rm, dims, ...) : object 'R_dense_rowSums' not found

[Chhiring-Lama]

Hi,

I am trying to run chromVAR on my bulk sequencing data from CUT&RUN. I am able to create a SummarizedExperiement Object. But I keep getting the Error in .local(x, na.rm, dims, ...) : object 'R_dense_rowSums' not found everytime I try anything dowstream like filtering or calculating background peaks.

Currently, I am using a count matrix that I got from running multiBamSummary from deeptools.

What am I doing wrong?

[Muedi]

Hi,

I encountered a similar problem when calling getBackgroundPeaks, or any doenstream task (I also encountered it when calling the filter function but didn't need it anyway, as when running the functions code, no peak was dropped).

I could get around the issue when calling the functions passing object=assay(rangedSummarizedExperiment_obj) instead of the summarizedExp object itself.

Hope this works for you too :)