run_myOTs {ROKET}R Documentation

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
)

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.

Value

A R numeric matrix of pairwise distances.


[Package ROKET version 1.0.0 Index]