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 1.0.0
Index]