search

Danko-Lab / BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
161 stars 46 forks source link

use sparse matrices instead of full matrices ? #58

Open rmontagn opened 1 year ago

rmontagn commented 1 year ago

Hello,

First thank you for your tool.

I am currently using Bayestools to perform deconvolution.

However, from some steps you need to convert your single cell reference to a full matrix format instead of a sparse matrix format.

As I am working with an atlas, I have to subset the data so I can't use the total information in my reference.

Do you consider, if feasible, enabling the use of sparse matrices in the future ? This would make BayesPrism even more user friendly and allow to use large datasets as reference with minimal resources.

Thank you.

tinyi commented 1 year ago

Dear User,

Thank you very much for your suggestion.

We will incorporate this feature in our next release. In the meantime, you may construct the reference profile by summing up reads in each cell state/type, and specify input.type="GEP".

Best,

Tinyi

On Tue, Aug 29, 2023 at 9:50 AM rmontagn @.***> wrote:

Hello,

First thank you for your tool.

I am currently using Bayestools to perform deconvolution.

However, from some steps you need to convert your single cell reference to a full matrix format instead of a sparse matrix format.

As I am working with an atlas, I have to subset the data so I can't use the total information in my reference.

Do you consider, if feasible, enabling the use of sparse in the future ? This would make BayesPrism even more user friendly and allow to use large datasets as reference with minimal resources.

Thank you.

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/58, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHSYP75ZBNQCQVND5273XXXXSHANCNFSM6AAAAAA4C7ZKFE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

rmontagn commented 1 year ago

Thank you very much for your answer !

I will do as you advised.

Best

GKild commented 10 months ago

Hi, I can see this issue was raised in August last year - just wanted to reiterate that it being able to use sparse matrices would be an excellent feature to have. Are you still updating the package and if so, is it still your plan to add sparse matrices? Is there a planned date for next release? Thank you!

tinyi commented 9 months ago

Sorry for the delay. The new version v2.2 now supports input of dgMatrix as the input of scRNA-seq reference.