Monocle3 garnett

Question

[odi]

I am trying to annotate my cells using garnett, but i keep getting this error at this stage.

Error: is(object = cds, class2 = "CellDataSet") is not TRUE.

Here is my code: library(garnett) library(org.Mm.eg.db) classifier <- readRDS("./mmLung_20191017.RDS")

trac <- classify_cells(trac, classifier, db = org.Mm.eg.db, cluster_extend = TRUE, cds_gene_id_type = "SYMBOL")

Please help me!

[fracarb8]

The message is telling you that trac is not a CellDataSet object. How did you create it? if you processed your data with an external tool (e.g. scanpy or seurat), you need to properly convert it to cds before running garnett.