plotPeak: plot read enrichment profiles at a specific peak for all...
In MMDiff: Statistical Testing for ChIP-Seq data sets

Description Usage Arguments Author(s) See Also Examples

plot read enrichment profiles at a specific peak for all specified samples.

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plotPeak(DBA, Peak.id, Sample.ids = NULL, NormMethod = 'DESeq',
        plot.input = TRUE, fieldname = "PeakRawHists",
        save2file = FALSE, fn.pics)

`DBA`	DBA object, after running getPeakProfiles Specifically, it uses the element MD, which should contain an element called according to fieldname.
`Peak.id`	integer specifying the index of the peak to be drawn.
`Sample.ids`	sample ids (as in Cfp1$samples$SampleID)
`NormMethod`	specify which normalization method should be used, currently only the 'DESeq' method [3] is implemented. Note, that unless NormMethod=NULL, getNormFactors has to be called first.
`plot.input`	TRUE, if the input (control) should be included on the plot
`fieldname`	name of list element in DBA$MD that is used for plotting of peak. (e.g. PeakRawHists)
`save2file`	if TRUE plot is saved to pdf file
`fn.pics`	name of pdf file, to which the plot will be saved to.

Gabriele Schweikert

getPeakProfiles, getNormFactors, plotHistDists

# load DBA objects with peak profiles 
data(Cfp1Profiles)
plotPeak(Cfp1Profiles, Peak.id=20, NormMethod=NULL)

# plot normalized profiles of WT.AB2 and Resc.AB2 samples,  don't plot
# the input:

Cfp1Norm <- getNormFactors(Cfp1Profiles)
Sample.ids <- c("WT.AB2", "Resc.AB2")
plotPeak(Cfp1Norm, Peak.id=20, Sample.ids=Sample.ids,
      NormMethod='DESeq', plot.input = FALSE)