setProjectIdentity: Set Project-Wide Cell Identity Variable

Sets the metadata column to use as the primary cell identity variable for all downstream analyses. This function establishes which cell grouping will be used in functions like findDESNPs() and other SNP analysis methods.

Arguments

ident_col: Character. Name of the column in cell_metadata to use as cell identity. Must be an existing column in the metadata.

Value

Returns the object invisibly (for method chaining).

Details

This function validates that the specified column exists in the cell metadata, then sets it as the active identity for all subsequent analyses. It also prints a summary of the unique identities found and the number of cells in each category.

The identity column is crucial for many analysis functions as it defines how cells are grouped when comparing SNP expression or presence between populations.

Common identity variables include cell type annotations, cluster IDs, condition labels, or any other categorical metadata that meaningfully separates cell populations.

Note

This function must be called before using analysis methods that rely on cell identities
The function prints a summary of the identities found, which can be useful for verification
The previously set identity (if any) is overwritten by this function

Examples


if (FALSE) { # \dontrun{

# Set cell type as the active identity

project$setProjectIdentity("cell_type")

# Use cluster IDs instead
project$setProjectIdentity("seurat_clusters")

# Set disease status as identity for case-control comparisons
project$setProjectIdentity("disease_status")

# Method chaining example
results <- project$setProjectIdentity("cell_type")$findDESNPs(
  ident.1 = "T_cells",
  donor_type = "Donor"
)
} # }