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ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
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A problem when using "CreateObject_fromSeurat()" #3

Open ylxie21 opened 3 years ago

ylxie21 commented 3 years ago

Thanks for developing this user-friendly tools! I am using cellcall through seurat object and I think that I met some slight errors.

  1. User can not define project name. This parameter is not transfered.
  2. When using CreateObject_fromSeurat() to read count data from a large seurat object, there's an error message which may be misleading:

"there is no slot: ", slot," in your seurat object in RNA assay"

Actually, the real error is that as.matrix() failed because of the large sparse matrix.

Thanks for your time!

ShellyCoder commented 3 years ago

Hi ylxie21,

Check the code you have mentioned, i comment directly on the code in CreateObject_fromSeurat() which is aimed to capture error messages. In taht way, user can discovery the root error conveniently. Appreciate for your response!

Best, Shelly