plotCounts {epigraHMM} | R Documentation

## Create a plot with the results from epigraHMM

### Description

'plotCounts()' plots read counts and peak regions from 'epigraHMM()'

### Usage

    plotCounts(
      object,
      ranges,
      hdf5 = metadata(object)$output,
      peaks = NULL,
      annotation = NULL
    )

### Arguments

`object` | an epigraHMMDataSet
`ranges` | a GRanges object or a pair of integers with the genomic corrdinates/windows to be plotted
`hdf5` | an optional character string with the hdf5 file path from 'epigraHMM'
`peaks` | an optional parameter with a GRanges object or a vector of logicals (with length equal to the number of rows in 'object') specifying the genomic corrdinates/windows with peaks
`annotation` | an optional parameter with a GRanges object or a vector of logicals (with length equal to the number of rows in 'object') specifying the genomic corrdinates/windows of an annotation track

### Details

If the input object contains the assay 'offset', reads will be normalized prior to plotting (e.g. counts/exp(offset)). Reads from replicates pertaining to the same condition are aggregated prior to plotting.

### Value

A ggplot

### Author(s)

Pedro L. Baldoni, pedrobaldoni@gmail.com

### References

https://github.com/plbaldoni/epigraHMM

### Examples

    countData <- rbind(matrix(rnbinom(1e3,mu = 2,size = 10),ncol = 1),
                       matrix(rnbinom(1e3,mu = 7.5,size = 5),ncol = 1),
                       matrix(rnbinom(1e3,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)

    plotCounts(object,ranges = c(500,3500))

[Package epigraHMM version 1.0.8 Index]