callPeaks {epigraHMM} | R Documentation

## Summarize peak calls and optionally create a BED 6+3 file in broadPeak format for visualization

### Description

This function imports the output from 'epigraHMM' and outputs a set of peaks (consensus or differential) for a given FDR control threshold or Viterbi sequence.

### Usage

    callPeaks(
      object,
      hdf5 = metadata(object)$output,
      method = "viterbi",
      saveToFile = FALSE,
      control = NULL
    )

### Arguments

`object` | an epigraHMMDataSet
`hdf5` | a character with the location of the epigraHMM HDF5 output file
`method` | either 'viterbi' or a numeric FDR control threshold (e.g. 0.05). Default is 'viterbi'.
`saveToFile` | a logical indicating whether or not to save the results to file. Output files are always saved with peaks of interest defined on the region level. Default is FALSE.
`control` | list of control arguments from controlEM(). This is an optional parameter and it is only required when 'saveToFile = TRUE' so that the output directory can be obtained. Default is NULL.

### Value

A GRanges object with differential peak calls in BED 6+3 format

### 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)

    rowRanges <- GenomicRanges::GRanges('chrA',
    IRanges::IRanges(start = seq(from = 1, length.out = 4e3,by = 250),width = 250))

    object <- epigraHMMDataSetFromMatrix(countData,colData,rowRanges)

    # Initializing
    object <- initializer(object,controlEM())

    # Running epigraHMM
    object <- epigraHMM(object,controlEM(),type = 'consensus',dist = 'nb')

    # Calling peaks
    peaks <- callPeaks(object = object,
                       hdf5 = S4Vectors::metadata(object)$output,
                       method = 'viterbi')

[Package epigraHMM version 1.0.8 Index]