PICS (version 2.16.0)

setParaEM: 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.

See Also

PICS