clustNEM {mnem} | R Documentation

## Cluster NEM.

### Description

This function clusters the data and performs standard nem on each cluster.

### Usage

    clustNEM(
      data,
      k = 2:10,
      cluster = NULL,
      starts = 1,
      logtype = 2,
      nem = TRUE,
      getprobspars = list(),
      getaffinitypars = list(),
      Rho = NULL,
      ...
    )

### Arguments

`data` | data of log ratios with cells in columns and features in rows
`k` | number of clusters to check
`cluster` | given clustering has to correspond to the columns of data
`starts` | number of random starts for the kmeans algorithm
`logtype` | logarithm type of the data
`nem` | if FALSE only clusters the data
`getprobspars` | list of parameters for the getProbs function
`getaffinitypars` | list of parameters for the getAffinity function
`Rho` | perturbation matrix with dimensions nxl with n S-genes and l samples; either as probabilities with the sum of probabilities for a sample less or equal to 1 or discrete with 1s and 0s
`...` | additional arguments for standard nem function

### Value

family of nems; the first k list entries hold full information of the standard nem search

`comp` | list of all adjacency matrices phi
`mw` | vector of mixture weights
`probs` | fake cell probabilities (see mw: mixture weights)

### Author(s)

Martin Pirkl

### Examples

    sim <- simData(Sgenes = 3, Egenes = 2, Nems = 2, mw = c(0.4,0.6))
    data <- (sim$data - 0.5)/0.5
    data <- data + rnorm(length(data), 0, 1)
    resulst <- clustNEM(data, k = 2:3)

[Package mnem version 1.8.0 Index]