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 |
LAMBDA2 |
A non-negative numeric value representing
the tuning parameter penalizing the distance between |
balance |
Boolean set to |
conv |
A positive numeric value to determine
algorithmic convergence. The default value is |
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 |
Value
A R numeric matrix of pairwise distances.