search

dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
266 stars 98 forks source link

fine.tune with new reference #43

Open drtrix90 opened 5 years ago

drtrix90 commented 5 years ago

Hello,

I've successfully made a new reference, and now I'm interested in creating more specific sub-types in this reference. How would I go about doing this? Is there a way to see how the build-in reference objects are structured? Does each main type require subtypes?

Thanks!

dviraran commented 5 years ago

The built references are all loaded with SingleR. Those are lists, and they are called - immgen, hpca, mouse.rnaseq and blueprint_encode. They all have the following fields: name; data (gene expression matrix); types and main_types - main_types is just a broader definition of types (i.e. samples of CD4+ T-cells and CD8+ T-cells in types can be T-cells in main_types); de.genes and de.genes.main - both created using the CreateVariableGeneSet. They also have a field called sd.thres, but this is only used for the sd mode, which you are probably not using. More information can be found here.

drtrix90 commented 5 years ago

Thank you. I'm a little confused as to how I would assign a group of types to a main type. They seem to just be independent lists in the vignette. Sorry if I'm missing something!

dviraran commented 5 years ago

Its just a broader definition, you also don't have to use it at all (there is a flag in the create functions to not do main types). Again, if in types you will define samples as subtypes of macrophages (M1,M2...) in main_types all those samples will be just macrophages.