info: Get information about peak calling results

In plbaldoni/epigrahmm: Epigenomic R-based analysis with hidden Markov models

Get information about peak calling results

Description

This function returns the BIC and expected log-likelihood function of the model, with respect to the last conditional distribution of unknown enrichment peaks given the data. The latter is also known as 'Q-function' in the EM context.

Usage

info(object)

Arguments

object

an epigraHMMDataSet

Value

A list with BIC, and expected log-likelihood function of the model. If the input object contains results from a differential analysis, 'info' will also output the enrichment patterns associated with each mixture component used in the mixture model.

Author(s)

Pedro L. Baldoni, [e-mail]

References

https://github.com/plbaldoni/epigraHMM

Examples

# Creating dummy object
countData <- rbind(matrix(rnbinom(1e3,mu = 2,size = 10),ncol = 1),
                   matrix(rnbinom(2e3,mu = 7.5,size = 5),ncol = 1),
                   matrix(rnbinom(1e3,mu = 2,size = 10),ncol = 1))

colData <- data.frame(condition = 'A', replicate = 1)
object <- epigraHMMDataSetFromMatrix(countData,colData)

# Initializing
object <- initializer(object,controlEM())

# Running epigraHMM
object <- epigraHMM(object,controlEM(),type = 'consensus',dist = 'nb')

# Get info
info(object)

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