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]