| 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 not a formal
S4 class (yet), the presence of certain list elements enables a
standardized approach to working with peaks identified from the data.
Slots/List Components
- name
- required character vector of length 1
unequivocally describing the peak, e.g. 'H3ac.chr8.peak1'
- chr
- required character vector of length one, naming the
chromosome of the peak, e.g. "8"
- start
- required integer of peak start position on the
chromosome, e.g. 60209200
- end
- required integer of peak start position on the
chromosome, e.g. 60209540
- cellType
- optional character vector describing the cell
type the ChIP chip experiment has been done on, e.g. "cellLine.HL1"
- modification
- required character vector describing the
modification or characteristic for which fragments were supposedly
enriched in immuno-precipitation step,
e.g. "H3ac" for acetylation of histone 3
- typeUpstream
- optional character vector of features that this
peak is located upstream of,
e.g. the transcriptional start site of "ENSMUST00000040104".
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. 1.74
- score
- optional numeric of a peak score, currently we use the
sum of smooted probe levels (log fold changes), e.g. 0.703
- 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. 1502 with name "ENSMUST00000040104"
- upSymbol
- optional character vector of gene symbols of
features the peak is located upstream of; supplements
typeUpstream; e.g. "Hand2"
- 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)
Tammo Krueger, Joern Toedling
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 = c("8"), winHalfSize = 400,
combineReplicates = TRUE)
peaksX <- findPeaksOnSmoothed(smoothX, probeAnno=exProbeAnno,
thresholds=1.5, allChr = c("8"),distCutOff=600)
peaksX <- relatePeaks(peaksX, exGFF)
str(peaksX[[2]])
[Package
Ringo version 1.2.0
Index]