Differential expression between two types of cells of specific marker gene expression
Take a look at the section "Finding Differentialy Expressed Feautres (cluster biomarkers)" of Seurat tutorial.

You have to define your clusters (if not computed automatically) by modifying the ident slot of the Seurat object.

Then you call the function FindMarkers of your Seurat object (to define markers of a given cluster against the rest) or FindAllMarkers (to look for all the combinations)