how to handle large dataset(>65000 cells) in scMetabolism?

[ybyOxidant]

Hello!
I am currently working with a dataset containing more than 60000 cells.
Runing sc.metabolism or sc.metabolism.Seurat is blocked by the ERROR below.
Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102

I believe it will happen when the column number exceeds the limitation of as.matrix(). So now I break the dataset into 2 parts to process by scMeatbolism, then merging them for downstream analysis. But it's not elegant, and the internal parameter of scMetabolism seems not equal. Do you have a better solution?

[wangshisheng]

Hello!

I meet same problem, could you provide some help? Many thanks~~

[abollol]

Hello! me too. any solution?

[honghh2018]

@wangshisheng @abollol same issue.
how to solve this problem?

[honghh2018]

What happen for this R package ? no one to maintain ?

[wu-yc]

This is limited by as.matrix(). You can split your datasets according to cell types (i.e. T cell, B cell, etc.) and perform the analysis one by one.