logLikelihoodcelda_CG {celda} | R Documentation

## Calculate Celda_CG log likelihood

### Description

Calculates the log likelihood for user-provided cell population and feature module clusters using the 'celda_CG()' model.

### Usage

    logLikelihoodcelda_CG(
      counts,
      sampleLabel,
      z,
      y,
      K,
      L,
      alpha,
      beta,
      delta,
      gamma
    )

### Arguments

`counts` | Integer matrix. Rows represent features and columns represent cells.
`sampleLabel` | Vector or factor. Denotes the sample label for each cell (column) in the count matrix.
`z` | Numeric vector. Denotes cell population labels.
`y` | Numeric vector. Denotes feature module labels.
`K` | Integer. Number of cell populations.
`L` | Integer. Number of feature modules.
`alpha` | Numeric. Concentration parameter for Theta. Adds a pseudocount to each cell population in each sample. Default 1.
`beta` | Numeric. Concentration parameter for Phi. Adds a pseudocount to each feature module in each cell population. Default 1.
`delta` | Numeric. Concentration parameter for Psi. Adds a pseudocount to each feature in each module. Default 1.
`gamma` | Numeric. Concentration parameter for Eta. Adds a pseudocount to the number of features in each module. Default 1.

### Value

The log likelihood for the given cluster assignments

### See Also

'celda_CG()' for clustering features and cells

### Examples

    data(celdaCGSim)
    loglik <- logLikelihoodcelda_CG(celdaCGSim$counts,
        sampleLabel = celdaCGSim$sampleLabel,
        z = celdaCGSim$z,
        y = celdaCGSim$y,
        K = celdaCGSim$K,
        L = celdaCGSim$L,
        alpha = celdaCGSim$alpha,
        beta = celdaCGSim$beta,
        gamma = celdaCGSim$gamma,
        delta = celdaCGSim$delta)

    loglik <- logLikelihood(celdaCGSim$counts,
        model = "celda_CG",
        sampleLabel = celdaCGSim$sampleLabel,
        z = celdaCGSim$z,
        y = celdaCGSim$y,
        K = celdaCGSim$K,
        L = celdaCGSim$L,
        alpha = celdaCGSim$alpha,
        beta = celdaCGSim$beta,
        gamma = celdaCGSim$gamma,
        delta = celdaCGSim$delta)

[Package celda version 1.2.4 Index]