dmmEM-methods {TFBSTools} | R Documentation

## dmmEM method

### Description

This function trains the Dirichlet multinomial mixture models parameters for a set of profile matrices.

### Usage

      dmmEM(x, K=6, alg=c("C", "R"))

### Arguments

`x` | x can be a `matrix`, `PFMatrixList` or `JASPAR2014` to be trained.
`K` | The maximal number of components to test in the mixture model when alg is "C". Then an optimal number of components between 1 and K will be chosen based on the fitness of the model. The fixed number of components to use when alg is "R". The default is 6.
`alg` | The algorithm to use. "C" uses the implementation from `DirichletMultinomial` package which has more advanced feature and performance. "R" uses our own implemention in R.

### Details

When using the implementation from `DirichletMultinomial` package, the final number of components can be 1:K. An internal selection will be made based on the maximum likelihood.

When using the implementation of R, the number of component is fixed to K.

### Value

A list of trainned alpha0, pmix and likelihood during the training.

### Methods

`signature(x = "ANY")`
`signature(x = "matrix")`
`signature(x = "PFMatrixList")`

### Author(s)

Ge Tan

### See Also

`rPWMDmm`

### Examples

        data(MA0003.2)
        data(MA0004.1)
        pfmList <- PFMatrixList(pfm1=MA0003.2, pfm2=MA0004.1, use.names=TRUE)
        dmmParameters <- dmmEM(pfmList, K=6, alg="C")

[Package TFBSTools version 1.18.0 Index]