I am learning the Seurat algorithms to cluster the scRNA-seq datasets. I found this explanation, but am confused. Can someone explain it to me, "The FindClusters function implements the procedure, and contains a resolution parameter that sets the ‘granularity’ of the downstream clustering, with increased values leading to a greater number of clusters. We find that setting this parameter between 0.6-1.2 typically returns good results for single cell datasets of around 3K cells". My questions are:
- What is "granularity" of the downstream analysis?
- How does the parameter "resolution" work?
- How to know the optimum value for parameter "resolution"?
I found this paper about the resolution that might help, but not clear to me yet. https://iopscience.iop.org/article/10.1088/1742-5468/2008/10/P10008/pdf.
I think the higher the resolution, the more clusters produced meaning the smaller clusters obtained? The smaller the clusters the more specific cell types we get, is that correct?