R crash when running leiden algorithm
Entering edit mode
11 weeks ago
Chris ▴ 230

Hi all,

I would like to run leiden algorithm using seurat but got R crash when chosing algorithm = 4. Scanpy doesn't have this issue but for the consistency of the plots, I want to use seurat. I appreciate your help! I guest the size of data is too big (14.5GiB) which casue the issue.

seurat.combined <- FindClusters(seurat.combined, resolution = 0.1, algorithm = 4)
Warning: sparse->dense coercion: allocating vector of size 14.5 GiB.   
NAs introduced by coercion to integer range.   
Warning: NAs introduced by coercion to integer rangeWarning in paste(condition$message, collapse = "\n") :
seurat • 245 views

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