controlEM {epigraHMM} | R Documentation |
This function passes controlling parameters for the EM algorithm implemented in the epigraHMM package.
controlEM( epsilonEM = c(MRCPE = 0.001, MACPE = 0.001, ARCEL = 0.001), maxIterEM = 500, minIterEM = 3, gapIterEM = 3, maxCountEM = 3, maxDisp = 1000, criterion = "all", minZero = .Machine$double.xmin, probCut = 0.05, quiet = TRUE, maxIterInnerEM = 5, epsilonInnerEM = 0.001, trimOffset = 3, pattern = NULL, tempDir = tempdir(), fileName = "epigraHMM", pruningThreshold = NULL, quietPruning = TRUE )
epsilonEM |
a named vector of positive values specifying up to four possible convergence criterion tolerances for the EM algorithm (see 'criterion' below). Default is c('MRCPE' = 1e-3, 'MACPE' = 1e-3,'ARCEL' = 1e-3). |
maxIterEM |
a positive integer giving the maximum number of EM iterations. Default is 500. |
minIterEM |
a positive integer giving the minimum number of EM iterations to start evaluating the convergence. Default is 3. |
gapIterEM |
a positive integer giving the number of EM iterations apart to compute the convergence criterion. Default is 3. |
maxCountEM |
a positive integer giving the number of consecutive EM iterations satisfying the convergence criterion in order to stop the algorithm. Default is 3. |
maxDisp |
a positive value for the upper limit constraint of the dispersion parameters. Default is 1000. |
criterion |
a character specifying the convergence criterion. Either "MRCPE" (maximum absolute relative change in parameter estimates), "MACPE" (maximum absolute change of parameter estimates), "ARCEL" (absolute relative change of the Q-function), or "all" (simultaneously check for MRCPE, MACPE, and ARCEL). Default is "all". |
minZero |
a positive value for the minimum positive value allowed in computations to avoid having zeros. Default is .Machine$double.xmin. |
probCut |
a number between 0 and 1 for the cutoff of the rejection controlled EM algorithm. Default 0.05. |
quiet |
a logical indicating whether to print messages. Default is TRUE. |
maxIterInnerEM |
a positive integer giving the maximum number of inner EM iterations. Default is 5. |
epsilonInnerEM |
a positive value with the convergence tolerance value for the inner EM algorithm. The criterion for the inner EM is "MRCPE". Default is 1e-3. |
trimOffset |
either NULL or a positive integer indicating the number of decimal places to be used in the offset. Default is 3. |
pattern |
either NULL (the default) or a list with length equal to the number of differential patterns to be modeled by the differential HMM state. See Details section below. |
tempDir |
a string where results will be saved. Default is 'tempdir()'. |
fileName |
a string with the name of the result files. Default is 'epigraHMM'. |
pruningThreshold |
a numeric value between 0 and 1 to consider when pruning rare combinatorial patterns. Default is NULL (see Details). |
quietPruning |
a logical indicating whether to print messages during the pruning step. Default is TRUE. |
If pattern
is NULL, every possible combinatorial pattern will be considered. If pattern
is a list, elements of it should specify the differential patterns to be modeled by each mixture component.
For instance, if pattern = list(2,c(1,3)) the mixture model will have two components that will represent the enrichment of condition 2 alone and the enrichment of conditions 1 and 3 together.
If pruningThreshold
is a value between 0 and 1, say 0.05, epigraHMM
will sequentially remove differential combinatorial patterns of enrichment
from any mixture model component with associated posterior mixture proportion
less than 0.05.
A list with components equal to the arguments
Pedro L. Baldoni, pedrobaldoni@gmail.com
https://github.com/plbaldoni/epigraHMM
# No more than 100 EM iterations control <- controlEM(maxIterEM = 100)