Convert or extract Seurat object as the input of FateID

Question

I am currently using Seurat to do the scRNA-seq clustering analysis. After this, I am planning to use FateID to do the downstream analysis, could someone teach me how to convert or extract a Seurat object as the input for FateID?

Thanks in advance.

Answer 1

Seurat objects have various slots where different types and forms of data are stored. For FateID you would need an expression matrix (with cells as columns and genes as rows) and this can be extracted via:

seurat_object@assays$RNA@data

Here RNA is the assay (you can have multiple assays per sample, RNA, protein, ...) and data is normalized data. You can extract counts or scaled data instead.

If you are using Seurat v2, drop the @assays$RNA part.