epigraHMM {epigraHMM} | R 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')

[Package epigraHMM version 1.0.8 Index]