EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data

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Improved_Seurat_Pre_Process String Idents

alperoglu opened this issue · comments

I suppose this is a minor issue that can be resolved simple data adjustments to the Seurat Object input. I am writing this as a future reference to other people that have the same issue.

The FindMarkers function uses 0 for the ident.1 argument and this causes issues with string identifiers. It gives the following error when the input cluster identifiers are strings:
Error in WhichCells.Seurat: Cannot find the following identities in the object: 0
I was using the output data from this Seurat tutorial : https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html

I changed the string identifiers to the seurat_cluster identifiers in the metadata that were the numeric equivalents of the cell type names.