AssignCellTypes: AssignCellTypes

In plevritis-lab/CELESTA: Cell type identification with spatial information

AssignCellTypes

Description

Find the cell types based on the scores (anchor cell) or probabilities (index cell)

Usage

AssignCellTypes(
  initial_pri_matrix,
  current_cell_prob,
  current_cell_type_assignment,
  marker_exp_prob,
  cell_type_num,
  unassigned_cells,
  round,
  high_marker_threshold,
  low_marker_threshold,
  min_difference = 0,
  min_prob = 0
)

Arguments

initial_pri_matrix	user defined cell-type marker matrix for a specific round
current_cell_prob	the current cell probability (number_cells x number_cell_type)
current_cell_type_assignment	the current cell type assignments (number_cells x total_rounds)
marker_exp_prob	the marker expression probability for each cell
cell_type_num	the cell types associated with the current round
unassigned_cells	cells not assigned a cell type for each round and iteration
round	the current round
high_marker_threshold	the upper threshold for each cell type
low_marker_threshold	the lower threshold for each cell type
min_difference	lower bound used to determine cells that meet the threshold
min_prob	lower bound used to determine cells that meet the threshold

Value

an updated current cell type assignment (number_cells x total_rounds) with more cells assigned for the current round

plevritis-lab/CELESTA documentation built on Jan. 30, 2023, 3:32 p.m.