Saving snap object

[mihbasad]

Is it possible to save a snap object (in .snap format) after filtering cells?

[r3fang]

Hi there,

Thank you for your question. Currently, it does not support that functionality. What would be the application for that if it is possible to extract any subset of cells using a snap file?

Best,

Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego

On Jul 8, 2019, at 12:12 PM, mihasad [email protected] wrote:

Is it possible to save a snap object (in .snap format) after filtering cells?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/56?email_source=notifications&email_token=ABT6GGZU2JH5Y7EEKWA44K3P6OGSFA5CNFSM4H66VCQKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G55V5TA, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG6OWDL4ERE262MOZYDP6OGSFANCNFSM4H66VCQA.

[mihbasad]

Hi

We used two samples in the same experiment. If I can separate cells from a snap object to create a new one, I would be able to separate two samples. Though I can separate them before running snaptool, I thought, it would be easier to separate from the snap object. Again if I can save my final dataset (combining all samples with filtered cell) as a snap object, loading / distributing the dataset would be easier.

Thanks Imam

[r3fang]

Hi,

Thanks for the clarification, I don’t know if i full understand our question. SnapATAC is able to subset or combined multiple samples easily. For example, this is one example to combine two samples with 2 snap files: https://github.com/r3fang/SnapATAC/blob/master/examples/10X_sci/README.md https://github.com/r3fang/SnapATAC/blob/master/examples/10X_sci/README.md

Also you can easily split a snap object into two: x1.sp = x.combined.sp[1:100,]; x2.sp = x.combined.sp[101:nrow(x.combined.sp),];

Does it answer your question?

-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego

On Jul 8, 2019, at 2:39 PM, mihasad [email protected] wrote:

Hi

We used two samples in the same experiment. If I can separate cells from a snap object to create a new one, I would be able to separate two samples. Though I can separate them before running snaptool, I thought, it would be easier to separate from the snap object. Again if I can save my final dataset (combining all samples with filtered cell) as a snap object, loading / distributing the dataset would be easier.

Thanks Imam

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/56?email_source=notifications&email_token=ABT6GG4TPSH5CYANOLEWLY3P6OXZRA5CNFSM4H66VCQKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZON23I#issuecomment-509402477, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG7AIL32R5OVWUB55QLP6OXZRANCNFSM4H66VCQA.

[mruffalo]

Hi-

It's true that "SnapATAC is able to subset or combined multiple samples easily", but this does not help in saving a subset of the data, after filtering or for one specific cluster, etc. This is very useful in sharing data with collaborators or passing it to other analysis tools.

This is the difference between telling someone "load this data file" and "load this data file and perform the same filtering that I did, with this large script, then select cells 10 through 250", and so on.

Can this be implemented any time soon?