clone_root — clone_root • Clonotrace

Identify Root Clone from Cluster Enrichment

Usage

clone_root(clones, cell_meta, clone_col, cluster_col, start_cluster)

Arguments

clones: A character vector of clone identifiers.
cell_meta: A data frame with clone and cluster information per cell.
clone_col: Name of the column containing clone labels.
cluster_col: Name of the column containing cluster labels.
start_cluster: Name or value of the cluster to define the root state.

Value

The name of the most enriched clone in the start cluster.

Details

Finds the most enriched clone in a given starting cluster, to use as a pseudotime root.

Examples

root_clone <- clone_root(clones = c("A", "B", "C"),
                         cell_meta = cell_metadata,
                         clone_col = "clone_id",
                         cluster_col = "cluster",
                         start_cluster = "Naive")
#> Error in clone_root(clones = c("A", "B", "C"), cell_meta = cell_metadata,     clone_col = "clone_id", cluster_col = "cluster", start_cluster = "Naive"): could not find function "clone_root"