controlEM: Control parameters for the EM algorithm from epigraHMM

In plbaldoni/mikado: What the package does (short line)

Description

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

Usage

controlEM(
  epsilon.em = 0.01,
  maxit.em = 15,
  minit.em = 1,
  maxcount.em = 1,
  windowSize = 100,
  pcut = 0.05,
  quiet = FALSE,
  chr = paste0("chr", 1:22),
  cores = 1,
  clusters = NULL,
  dir = tempdir(check = TRUE),
  fdr = 0.1,
  init = "fast"
)

Arguments

epsilon.em	Add description here
maxit.em	a positive integer giving the maximum number of EM iterations. Default is 500.
minit.em	a positive integer giving the minimum number of EM iterations to start evaluating the convergence. Default is 3.
maxcount.em	a positive integer giving the number of consecutive EM iterations satisfying the convergence criterion in order to stop the algorithm. Default is 3.
windowSize	the proportion of the genome to use as window in the sliding window initialization
pcut	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.
chr	chromosomes for initialization
cores	number of cores to use
clusters	number of clusters to detect
dir	directory with files will be saved
fdr	the FDR level to call peaks (default if 0.10)
init	either 'HMM' or 'fast' (default is 'fast')

Details

Add details here

Value

A list with components equal to the arguments

Author(s)

Pedro L. Baldoni, [e-mail]

References

https://github.com/plbaldoni/mikado

Examples

# No more than 100 EM iterations
control <- controlEM(maxit.em = 100)

plbaldoni/mikado documentation built on June 9, 2020, 3:34 p.m.