Closed JH1606-code closed 2 years ago
Hi @JH1606-code
Thanks for having been interested in our tool. This problem is because a large number of features in the tirosh_mel80_example were removed, in order to have a small example dataset ship with the package. To make the vignettes work, the remained features are the ones used by those three models (B cells, T cells, and NK).
To use all the classifiers, I suggest you use another (public) dataset where there are features available for other cell-type classifiers.
Hope this helps. Bests, Vy
Thanks for your fast answer. This helps a lot!
Hi,
thanks for this nice tool but I have a problem to do the analysis of my data with the parameter cell_types = "all". If I use your test sample of the tutorial (https://bioconductor.org/packages/devel/bioc/vignettes/scAnnotatR/inst/doc/classifying-cells.html) with the following parameter everything went fine:
seurat.obj <- classify_cells(classify_obj = tirosh_mel80_example, assay = 'RNA', slot = 'counts', cell_types = c('B cells', 'NK', 'T cells'), path_to_models = 'default')
But if I change the cell_types to "all" then I get the following error:
seurat.obj <- classify_cells(classify_obj = tirosh_mel80_example, assay = 'RNA', slot = 'counts', cell_types = 'all', path_to_models = 'default')
Error: snapshotDate(): 2021-10-20 loading from cache Error in marker_genes(x) : try to request a slot "marker_genes" from an object of simple class ("NULL") without slots
Do you have any idea how to fix this problem?
Best