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.
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maxK |
An integer . The maximum number of binding events per region. If the value is 0, the maximum number is automatically calculated.
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tol |
A numeric . The tolerance for the EM algorithm.
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B |
An integer . The maximum number of iterations to be used.
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mSelect |
A character string specifying the information criteria to be used when selecting the number of binding events.
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mergePeaks |
A logical stating whether overlapping binding events should be picked.
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mapCorrect |
A logical stating whether mappability profiles should be incorporated in the estimation, i.e: missing reads estimated.
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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).
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Value
Returns a list of parameters to be used in PICS.
Author(s)
Renan Sauteraud
See Also
PICS
[Package
PICS version 2.26.0
Index]