logLikelihoodByIter: Plots log likelihood in the models per iteration.

In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

Plots log likelihood in the models per iteration.

Description

Plots the log likelihood of the different models through iterations. Log likelihood after burnin should be stable, otherwise more iterations may be required (together with an increase in the burnin).

Usage

logLikelihoodByIter(object, select = NULL, ...)

Arguments

object	Initialized cisTopic object, after running runCGSModels.
select	Plot log-likelihood per iteration for selected topics (as a vector with the number of topics per model).
...	Ignored.

Value

Plots the log likelihood of the models thorugh the different iterations after burnin.

Examples

bamfiles <- c('example_1.bam', 'example_2.bam', 'example_3.bam')
regions <- 'example.bed'
cisTopicObject <- CreatecisTopicObjectfromBAM(bamfiles, regions)
cisTopicObject <- runCGSModels(cisTopicObject)
cisTopicObject <- logLikelihoodByIter(cisTopicObject)

aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.