Choose k per population from the reference group's cells

Choose k per population from the reference group's cells

Usage

choose_subcluster_k(
  cells,
  markers,
  group_col = "cohort",
  reference = NULL,
  k_range = 2:5,
  min_ref = 150L,
  seed = 42L
)

Arguments

cells

Embedded cell table: one row per cell, carrying umap_1/umap_2, sample_id, population_label and one column per marker.

markers

Character vector of marker names to use.

group_col

Name of the column holding the biological grouping (cohort). Default "cohort".

reference

The group every other group is compared against.

k_range

Candidate values of k to score. Default 2:5.

min_ref

Minimum reference-group cells required to fit. Default 150L.

seed

Random seed. The RNG stream is restored afterwards, so this cannot perturb later sampling. Default 42L.

Value

list(k = named integer population -> k, curve = data.frame of scores)