MMDiff (version 1.8.0)

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

Description

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

Usage

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

Arguments

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.

See Also

getPeakProfiles, getNormFactors, plotHistDists

Examples

# 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)