Build full-coverage gating tree
Usage
build_fullcoverage_tree(
expr_mat,
markers_pos,
markers_neg = character(0),
cell_idx = seq_len(ncol(expr_mat)),
depth = 0,
max_depth = 4,
min_cells = 200,
min_score = 0.5,
cutoff_method = c("mean", "equal_posteriors"),
gmm_model_names = NULL
)
Arguments
- expr_mat
expression matrix
- markers_pos
positive markers
- markers_neg
negative markers
- cell_idx
indices
- depth
depth
- max_depth
max depth
- min_cells
minimum cells
- min_score
minimum separability
- cutoff_method
Cutoff selection method passed to [fit_gmm_2()].
- gmm_model_names
Optional character vector of model names to pass to
[mclust::Mclust()] (e.g., "V" to forbid equal-variance in 1D).
Examples
set.seed(1)
expr_mat <- rbind(
CD3 = c(rnorm(50, 0, 0.2), rnorm(50, 2, 0.2)),
CD20 = c(rnorm(50, 2, 0.2), rnorm(50, 0, 0.2))
)
tree <- build_fullcoverage_tree(
expr_mat,
markers_pos = c("CD3", "CD20"),
max_depth = 2,
min_cells = 20,
min_score = 0.1
)
tree$type
#> [1] "node"
