peak {Ringo}R Documentation

Class peak - A list holding ChIP-chip peak characteristics

Description

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.

Slots/List Components

name
required character vector of length 1 unequivocally describing the peak, e.g. "Suz12.Nudt2.upstream.peak"
chr
required character vector of length one, naming the chromosome of the peak, e.g. "9"
start
required integer of peak start position on the chromosome, e.g. 34318900
end
required integer of peak start position on the chromosome, e.g. 34320100
cellType
optional character vector describing the cell type the ChIP chip experiment has been done on, e.g. "human"
antibody
required character vector describing the antibody or characteristic for which fragments were supposedly enriched in immuno-precipitation step, e.g. "Suz12" for the protein Suz12
typeUpstream
optional character vector of features that this peak is located upstream of, e.g. the transcriptional start site of "ENST00000379158". See relatePeaks for details.
typeDownstream
optional character vector of features that this peak is located downstream of
maxPeak
optional numeric of maximal (smoothed) probe level in the peak, e.g. 2.00
score
optional numeric of a peak score, currently we use the sum of smoothed probe levels (log fold changes), e.g. 69.16
probes
optional character vector of probe identifiers of all probes with match positions in the peak
distMid2TSS
optional named numeric vector of distances of the peak middle position to features, e.g. TSSs of transcripts up- and downstream; names are the features to which the distances are given; only meaningful in combination with typeUpstream and typeDownstram; e.g. 55 with name "ENST00000379158"
upSymbol
optional character vector of gene symbols of features the peak is located upstream of; supplements typeUpstream; e.g. "Nudt2"
downSymbol
optional character vector of gene symbols of features the peak is located upstream of; supplements typeDownstream.
...
further list elements can be added like normal list elements.

Creation

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

Methods defined for lists of class peak are print.peak and plot.peak.

peakList

A list in which each element is of class peak, is called a peakList. This class, however, is not much in use yet.

Author(s)

Joern Toedling, Tammo Krueger, PT Bote

See Also

plot.peak, findPeaksOnSmoothed, relatePeaks

Examples

  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]])

[Package Ringo version 1.2.0 Index]