setParaEM {PICS} | R Documentation

## List of parameters for the EM algorithm that can be used as an argument of PICS.

### Description

This function takes from 0 to 7 EM algorithm parameters as argument, check if they are valid and returns a list to be used in a call to PICS.

### Usage

    setParaEM(
      minK = 1,
      maxK = 15,
      tol = 1e-04,
      B = 100,
      mSelect = "BIC",
      mergePeaks = TRUE,
      mapCorrect = TRUE,
      dataType = NULL
    )

### Arguments

`minK` | An `integer`. The minimum number of binding events per region. If the value is 0, the minimum number is automatically calculated.
`maxK` | An `integer`.The maximum number of binding events per region. If the value is 0, the maximum number is automatically calculated.
`tol` | A `numeric`. The tolerance for the EM algorithm.
`B` | An `integer`. The maximum number of iterations to be used.
`mSelect` | A `character`. pecifying the information criteria to be used when selecting the number of binding events.
`mergePeaks` | A `logical` stating whether overlapping binding events should be picked.
`mapCorrect` | A `logical` stating whether mappability profiles should be incorporated in the estimation, i.e: missing reads estimated.
`dataType` | A `character`. If a dataType is set, the algorithm will use the default parameters for this type of data (all the previous arguments will be ignored).

### Value

A `list` of parameters to be used in `PICS`.

### See Also

PICS setParaPrior

[Package PICS version 2.36.0 Index]