run_myOTs: run_myOTs

Description

run_myOTs

Usage

run_myOTs(
  ZZ,
  COST,
  EPS,
  LAMBDA1,
  LAMBDA2 = NULL,
  balance,
  conv = 1e-05,
  max_iter = 3000,
  ncores = 1,
  verbose = TRUE,
  show_iter = 50
)

Value

A R numeric matrix of pairwise distances.

Arguments

ZZ: A numeric matrix of non-negative mass to transport. Rows correspond to features (e.g. genes) and columns correspond to samples or individuals. Each column must have strictly positive mass
COST: A numeric square matrix of non-negative values representing the non-negative costs to transport masses between pairs of features
EPS: A positive numeric value representing the tuning parameter for entropic regularization.
LAMBDA1: A non-negative numeric value representing the tuning parameter penalizing the distance between XX and the row sums of the optimal transport matrix.
LAMBDA2: A non-negative numeric value representing the tuning parameter penalizing the distance between YY and the column sums of the optimal transport matrix.
balance: Boolean set to TRUE to run balanced optimal transport regardless of LAMDA1 and LAMBDA2. Otherwise run unbalanced optimal transport.
conv: A positive numeric value to determine algorithmic convergence. The default value is 1e-5.
max_iter: A positive integer denoting the maximum iterations to run the algorithm.
ncores: A positive integer for the number of cores/threads to reduce computational runtime when running for loops
verbose: Boolean value to display verbose function output.
show_iter: A positive integer to display iteration details at multiples of show_iter but only if verbose = TRUE.