initializer: Initializer of epigraHMM

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

Initializer of epigraHMM

Description

This function call enriched windows individually for each sample in an epigraHMMDataSet. These are then used for initializing purposes in epigraHMM. By default, the Viterbi algorithm is used to determine enriched windows. Input controls and normalizing offsets are not utilized in this initialization step.

Usage

initializer(object, control)

Arguments

object	an epigraHMMDataSet
control	list of control arguments from controlEM()

Details

To be added

Value

An epigraHMMDataSet with a 'peaks' assay filled in.

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())

# Visualizing initialization peaks
#plot(assay(object),type = 'l')
#lines(7.5*assay(object,'peaks'),col = 'red')

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