initializer {epigraHMM} | R Documentation

## 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, 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())

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

[Package epigraHMM version 1.0.8 Index]