factorize {ccfindR} | R Documentation

## Maximum likelihood factorization

### Description

Performs single or multiple rank NMF factorization of count matrix using maximum likelihood

### Usage

    factorize(object, ranks = 2, nrun = 20, randomize = FALSE,
      nsmpl = 1, verbose = 2, progress.bar = TRUE, Itmax = 10000,
      ncnn.step = 40, criterion = "likelihood", linkage = "average",
      Tol = 1e-05, store.connectivity = FALSE)

### Arguments

`object` | `scNMFSet` object containing count matrix.
`ranks` | Rank for factorization; can be a vector of multiple values.
`nrun` | No. of runs with different initial guess.
`randomize` | Boolean; if `TRUE`, input matrix is randomized.
`nsmpl` | No. of randomized samples to average over.
`verbose` | The verbosity level: 3, each iteration output printed; 2, each run output printed; 1, each randomized sample output printed; 0, silent.
`progress.bar` | Display progress bar when `nrun > 1` and `verbose = 1`.
`Itmax` | Maximum no. of iteration.
`ncnn.step` | Minimum no. of steps with no change in connectivity matrix to achieve convergence.
`criterion` | If `'likelihood'`, iteration stops when fractional changes in likelihood is below tolerance `Tol`. If `criterion = 'connectivity'`, iteration stops when connectivity matrix does not change for at least `ncnn.step` steps.
`linkage` | Method to be sent to `hclust` in calculating cophenetic correlation.
`Tol` | Tolerance for checking convergence with `criterion = 'likelihood'`.
`store.connectivity` | Returns a list also containing connectivity data.

### Details

The main input is the `scNMFSet` object with count matrix. This function performs non-negative factorization and fills in the empty slots `basis`, `coeff`, and `ranks`.

When run with multiple values of `ranks`, factorization is repeated for each rank and the slot `measure` contains quality measures of the ranks. The quality measure `likelihood` is negative the KL distance of the fit to the target. With `nrun > 1`, the likelihood is the maximum among all runs.

The quality measure `dispersion` is the scalar measure of how far the connectivity matrix is from 0, 1. With increasing `nrun`, `dispersion` decreases from 1. `nrun` should be chosen such that `dispersion` does not change appreciably. With randomization, `count` matrix of `object` is shuffled. `nsmpl` can be used to average over multiple permutations. This averaging applies to each quality measure under a given rank.

### Value

Object of class `scNMFSet` with factorization slots filled.

### Examples

    set.seed(1)
    x <- simulate_data(nfeatures=10,nsamples=c(20,20,60,40,30))
    s <- scNMFSet(count=x)
    s <- factorize(s,ranks=seq(2,8),nrun=5)
    plot(s)

[Package ccfindR version 1.10.0 Index]