GetCMS.RdCompute CMS scores (for cells of a single sample) from a multi-sample Seurat object. Requires a Seurat object with cell classifications stored as "Cell_Type" in the metadata and with sample ID stored as "orig.ident" in the metadata. Also requires a dataframe containing the "reference" cell classifications generated from the single-sample dataset. A single score on a scale of 0-1 is returned.
GetCMS(object = NULL, sample.ID = NULL, reference.ID = NULL)
| object | A multi-sample Seurat object with sample identifiers stored as "orig.ident" and cell classifications as "Cell_Type" in the object metadata slot. |
|---|---|
| sample.ID | The name of the single sample to be CMS-scored (must correspond to an ID stored in "orig.ident"). |
| reference.ID | A dataframe consisting of a single column, "Cell_Type", containing the cell classifications generated during a single-sample workflow (for use as a reference set without multi-sample batch effects).; |
Returns a numeric score from 0-1 (best-worst).
# NOT RUN { GetCMS(object = my_seurat_object, sample.ID = "PBMC_01", reference.ID = PBMC01_SingleSample_RefID) #> Error in GetCMS(object = my_seurat_object, sample.ID = "PBMC_01", reference.ID = PBMC01_SingleSample_RefID) object 'my_seurat_object' not found # }