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omnideconv / SimBu

Simulate pseudo-bulk RNAseq samples from scRNAseq expression data
http://omnideconv.org/SimBu/
GNU General Public License v3.0
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Bug in defining cell_id_col and cell_type_col in dataset_seurat function #43

Closed orange-whale closed 1 year ago

orange-whale commented 1 year ago

Hi

Thank you very much for this great tool!

I've experienced a bug in the dataset_seurat function for converting a seurat object to a SummarizedExperiment object. From the manual https://bioconductor.org/packages/devel/bioc/manuals/SimBu/man/SimBu.pdf it appears that you should be able to use the original column name for the ID and cell-type columns in the seurat metadata slot, but when i tried that the function did not work. When I instead changed the name of those to columns to ID and cell_type the function worked again.

Best regards

alex-d13 commented 1 year ago

Hi,

Thanks for using Simbu :) Sorry, I might have missed your issue previously. Should be fixed in the next bioconductor update.

Best, Alex