plotPeaks: Create a plot of ChIP read counts with called peaks and...

In plbaldoni/mixNBHMM: Differential Peak Calling via Hidden Markov Model With Mixture of Negative Binomial Distributions

Description

'plotPeaks()' imports the output from 'mixNBHMM()' and plots the peak calls of a given genomic region. If the mixNBHMMDataSet 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.

Usage

plotPeaks(object, ranges, type = "viterbi", palette = "Set1")

Arguments

object	a mixNBHMMDataSet
ranges	a GRanges object with the genomic corrdinates to be plotted (e.g. GRanges('chr19',IRanges(50630740,50946896)))
type	either 'viterbi' (default) or an FDR control threshold (e.g. 0.05)
palette	the color brewer palette to be used (default is 'Set1')

Value

A ggplot

Author(s)

Pedro L. Baldoni, [e-mail]

References

https://github.com/plbaldoni/mixNBHMM

Examples

data(ENCODE)
ENCODE <- createOffset(object = ENCODE,type = 'loess',span = 1)
## Not run: ENCODE <- mixNBHMM(object = ENCODE,control = controlEM())
## Not run: plotPeaks(object = ENCODE,ranges = GRanges('chr2',IRanges(168750000,169200000)))

plbaldoni/mixNBHMM documentation built on Dec. 24, 2019, 1:31 p.m.