enve.recplot2.findPeaks.em: Enveomics: Recruitment Plot (2) Em Peak Finder

In enveomics.R: Various Utilities for Microbial Genomics and Metagenomics

Enveomics: Recruitment Plot (2) Em Peak Finder

Description

Identifies peaks in the population histogram using a Gaussian Mixture Model Expectation Maximization (GMM-EM) method.

Usage

enve.recplot2.findPeaks.em(
  x,
  max.iter = 1000,
  ll.diff.res = 1e-08,
  components = 2,
  rm.top = 0.05,
  verbose = FALSE,
  init,
  log = TRUE
)

Arguments

x	An enve.RecPlot2 object.
max.iter	Maximum number of EM iterations.
ll.diff.res	Maximum Log-Likelihood difference to be considered as convergent.
components	Number of distributions assumed in the mixture.
rm.top	Top-values to remove before finding peaks, as a quantile probability. This step is useful to remove highly conserved regions, but can be turned off by setting rm.top=0. The quantile is determined after removing zero-coverage windows.
verbose	Display (mostly debugging) information.
init	Initialization parameters. By default, these are derived from k-means clustering. A named list with vectors for mu, sd, and alpha, each of length components.
log	Logical value indicating if the estimations should be performed in natural logarithm units. Do not change unless you know what you're doing.

Value

Returns a list of enve.RecPlot2.Peak objects.

Author(s)

Luis M. Rodriguez-R [aut, cre]

enveomics.R documentation built on April 3, 2025, 9:06 p.m.