setParaEM {PICS} | R Documentation

## Function that returns a 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-4,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 string specifying 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

Returns a list of parameters to be used in PICS.

### Author(s)

Renan Sauteraud

### See Also

`PICS`

[Package PICS version 2.28.0 Index]