Gene names VS gene IDs in precomputed models about celltypist

[ChuanXu1]

@emdann

1. information relating to no-feature overlap is logged and output after version 0.2.0 #15
2. good suggestion! will add this

[emdann]

brilliant! Thank you

[ChuanXu1]

@emdann, as I tested, some Ensembl IDs can match multiple gene symbols, it's not so intuitive to store Ensembl IDs along with gene symbols in a single model. Moreover, as well as Ensembl IDs, the users may have other needs (HGNC ID, old gene symbols, etc.)

Therefore, there is a convert method, which is initially designed to convert human/mouse model to mouse/house model by mapping orthologous genes. This method can be also used for the Ensembl ID case, where the users provide a map file to convert the genes in the model to other formats (Ensembl IDs, HGNC, orthologous genes, ...)

model = celltypist.Model.load("some_model.pkl")
model.convert(map_file = 'symbol2ID.csv') #the map file provided by the user based on what they'd like to transform the gene symbols to
model.write("/path/to/converted_some_model.pkl")

I think this should be a better way to deal with the case you encounter.

Also see the Usage -> Supplemental guidance -> Cross-species model conversion