R crash with large datasets

[rmathieu25]

Hello,

Thank you for this package that seems very useful.

Nevertheless, I have an integrated datasets with 150 000 cells, and my R crash when calculating the co-clustering frequencies. I have a computer with a RAM memory of 128 GB. My integrated dataset takes up 15.4GB. Do you have any idea how could I overcome this issue.

Thank you in advance

[MenonLab]

Hi there,

Thanks for mentioning this - we have not yet optimized chooseR for very large data sets, but will let you know when we update the code to allow for that. In the meantime, is there any substructure at the top level of your data set? If there are clearly discrete subgroups of cells at the top level, you could run chooseR separately on these subsets - usually, the subsets are also where there is more confusion about what parameter values are the most robust.

Also, we have forked the development version of the code here:
https://github.com/MenonLab/chooseR
We hope to have the updated, more memory-efficient version soon.

[rmathieu25]

Hello,

Thank you for your answer.

I was thinking to run chooseR on subsets so I will give it a try.

Thank you.