DeconX: This function updates decontamination

In compbiomed/celda: CEllular Latent Dirichlet Allocation

Description

This function updates decontamination

Usage

DeconX(omat, z = NULL, max.iter = 200, beta = 1e-06, delta = 10,
  logfile = NULL, verbose = TRUE, seed = 1234567)

Arguments

omat	Numeric/Integer matrix. Observed count matrix, rows represent features and columns represent cells.
z	Integer vector. Cell population labels. Default NULL
max.iter	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 set.seed(). Default to be 1234567

Examples

decon.c = DeconX( omat = contamination.sim$rmat + contamination.sim$cmat, z=contamination.sim$z, max.iter=3)
decon.bg = DeconX( omat=contamination.sim$rmat + contamination.sim$cmat, max.iter=3 ) 

compbiomed/celda documentation built on May 25, 2019, 3:58 a.m.