epigraHMM: Perform peak calling of epigenomic data sets

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

Perform peak calling of epigenomic data sets

Description

This function runs either consensus (one condition, multiple samples) or differential (multiple conditions and samples) peak callers for epigenomic data.

Usage

epigraHMM(object, control, type, dist = "nb")

Arguments

object	an epigraHMMDataSet
control	list of control arguments from controlEM
type	character, either "consensus" or "differential"
dist	character, either "zinb" or "nb" (default)

Value

An epigraHMMDataSet object with the results from epigraHMM

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')

plbaldoni/epigraHMM documentation built on Oct. 15, 2023, 7:53 p.m.