Set Selected Features for Ordering — set_selected

This function updates the internal metadata of a Monocle3 (cell_data_set) or Seurat object to mark specific genes as use_for_ordering. This is useful for defining a custom set of features for trajectory inference.

Usage

set_selected_features(cds, genes, gene_column = "id", unique_column = "id")

Arguments

cds: An object of class cell_data_set (Monocle3) or Seurat.
genes: Character vector. A list of gene identifiers to mark as selected. These must match the identifiers found in gene_column.
gene_column: Character. The name of the column in the object's dispersion metadata to match against the provided genes vector. Default is "id".
unique_column: Character. Used only for Monocle3 objects with a dispersion function present. Specifies the unique identifier column in the dispersion table to map back to if gene_column is being used for lookup (e.g., mapping gene symbols back to Ensembl IDs). Default is "id".

Value

The modified cds object with the updated use_for_ordering slot.

Details

Manually defines the set of features (genes) to be used for trajectory ordering or downstream analysis.

Examples

if (FALSE) { # \dontrun{
  # Define a list of interesting genes
  my_genes <- c("GeneA", "GeneB", "GeneC")

  # Update the object to use these genes for ordering
  cds <- set_selected_features(cds, genes = my_genes)
} # }