epigraHMM: Perform peak calling of epigenomic data sets

View source: R/epigraHMM.R

epigraHMMR Documentation

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, pedrobaldoni@gmail.com

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.