| peak {Ringo} | R Documentation |
An object of class peak is a list holding characteristics of an
enrichment peak from ChIP chip data. While this is only a S3 rather
than a formal S4 class (yet), the presence of certain list
elements enables a standardized approach to working with enriched
regions identified from ChIP-chip data.
Note that the term "peak", while commonly used in ChIP-chip context,
is slightly misleading and the term "ChIP-enriched region" would be
more appropriate. Within such regions the actual signal could show two
or more actual signal peaks or none at all (long plateau). For
succinctness sake, we use the term "peak" for a ChIP-enriched region,
though.
relatePeaks for details.typeUpstream and
typeDownstram; e.g. 55 with name "ENST00000379158"typeUpstream; e.g. "Nudt2" typeDownstream.
Objects of class peak are created by other functions,
such as findPeaksOnSmoothed; or by creating a list with
the respective components and assigning it the class peak,
which is essentially, what the function newPeak does.
Methods defined for lists of class peak are
print.peak and plot.peak.
A list in which each element is of class peak, is called
a peakList. This class, however, is not much in use yet.
Joern Toedling, Tammo Krueger, PT Bote
plot.peak, findPeaksOnSmoothed,
relatePeaks
exDir <- system.file("exData",package="Ringo")
load(file.path(exDir,"exampleProbeAnno.rda"))
load(file.path(exDir,"exampleX.rda"))
smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
modColumn = "Cy5", allChr = "9", winHalfSize = 400)
peaksX <- findPeaksOnSmoothed(smoothX, probeAnno=exProbeAnno,
thresholds=0.45, allChr="9", distCutOff=600)
peaksX <- relatePeaks(peaksX, exGFF)
str(peaksX[[1]])