decontX {celda}R Documentation

Decontaminate count matrix

Description

This function updates decontamination on dataset with multiple batches.

Usage

decontX(counts, z = NULL, batch = NULL, maxIter = 200, delta = 10,
  logfile = NULL, verbose = TRUE, seed = 12345)

Arguments

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.

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.

Value

A list object which contains the decontaminated count matrix and related parameters.

Examples

data(contaminationSim)
deconC <- decontX(
  counts = contaminationSim$rmat + contaminationSim$cmat,
  z = contaminationSim$z, maxIter = 3
)
deconBg <- decontX(
  counts = contaminationSim$rmat + contaminationSim$cmat,
  maxIter = 3
)

[Package celda version 1.0.4 Index]