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 1.2.4 Index]