Default parameters for Harmony batch correction

Usage

params_sc_harmony(
  k = NULL,
  sigma = 0.1,
  theta = 2,
  lambda = 1,
  block_size = 0.05,
  max_iter_kmeans = 20L,
  max_iter_harmony = 10L,
  epsilon_kmeans = 1e-05,
  epsilon_harmony = 1e-04,
  window_size = 2L
)

Arguments

k: Optional integer. Number of clusters for k-means clustering. If not provided, it will be automatically determined as min(round(N / 30), 200).
sigma: Numeric vector. Per-cluster diversity weights. Either a single value (broadcast to all clusters) or a vector of length k.
theta: Numeric vector. Per-variable diversity penalties. Either a single value (broadcast to all variables) or a vector of length equal to the number of batch variables.
lambda: Numeric vector. Ridge regression penalty for the linear model. Typically a single value that is broadcast to all design matrix columns.
block_size: Numeric. Fraction of cells to update per block during optimisation (0.0-1.0). Lower values reduce memory usage but increase computation time.
max_iter_kmeans: Integer. Maximum number of k-means iterations per Harmony round.
max_iter_harmony: Integer. Maximum number of Harmony outer iterations.
epsilon_kmeans: Numeric. Convergence threshold for k-means clustering. Stops when the relative change in cluster assignments falls below this value.
epsilon_harmony: Numeric. Convergence threshold for Harmony. Stops when the relative change in the objective function falls below this value.
window_size: Integer. Number of previous iterations to consider when checking convergence.

Value

A list with the parameters.