controlEM: Control parameters for the EM algorithm from epigraHMM

View source: R/controlEM.R

controlEMR Documentation

Control parameters for the EM algorithm from epigraHMM

Description

This function passes controlling parameters for the EM algorithm implemented in the epigraHMM package.

Usage

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
)

Arguments

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.

Details

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.

Value

A list with components equal to the arguments

Author(s)

Pedro L. Baldoni, pedrobaldoni@gmail.com

References

https://github.com/plbaldoni/epigraHMM

Examples

# No more than 100 EM iterations
control <- controlEM(maxIterEM = 100)


plbaldoni/epigrahmm documentation built on Oct. 14, 2023, 5:13 a.m.