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]