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GreenleafLab / chromVAR

chromatin Variability Across Regions (of the genome!)
https://greenleaflab.github.io/chromVAR/
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Peaks without overlapping reads #30

Open timydaley opened 6 years ago

timydaley commented 6 years ago

Hi, When doing downstream analysis we remove cells that we do not trust, and after resizing this can result in peaks without any overlapping reads. It seems that chromVAR does not like this and returns the error Error in FUN(X[[i]], ...) : assay colnames() must be NULL or equal colData rownames()

AliciaSchep commented 6 years ago

Can you provide a bit more context? What function leads to this error? By resizing, do you mean that some cells are dropped, or that some peaks are dropped as well?