decontX {celda} | R Documentation |
This function updates decontamination on dataset with multiple batches.
decontX(counts, z = NULL, batch = NULL, maxIter = 200, beta = 1e-06, delta = 10, logfile = NULL, verbose = TRUE, seed = 12345)
counts |
Numeric/Integer matrix. Observed count matrix, rows represent features and columns represent cells. |
z |
Integer vector. Cell population labels. Default NULL. |
batch |
Integer vector. Cell batch labels. Default NULL. |
maxIter |
Integer. Maximum iterations of EM algorithm. Default to be 200. |
beta |
Numeric. Concentration parameter for Phi. Default to be 1e-6. |
delta |
Numeric. Symmetric concentration parameter for Theta. Default to be 10. |
logfile |
Character. Messages will be redirected to a file named 'logfile'. If NULL, messages will be printed to stdout. Default NULL. |
verbose |
Logical. Whether to print log messages. Default TRUE. |
seed |
Integer. Passed to with_seed. For reproducibility, a default value of 12345 is used. If NULL, no calls to with_seed are made. |
A list object which contains the decontaminated count matrix and related parameters.
data(contaminationSim) deconC <- decontX(counts = contaminationSim$rmat + contaminationSim$cmat, z = contaminationSim$z, maxIter = 3) deconBg <- decontX(counts = contaminationSim$rmat + contaminationSim$cmat, maxIter = 3)