cher-class {Ringo} | R Documentation |
An object of class cher
(ChIP-enriched region) holds
characteristics of an enriched genomic region from ChIP chip
data.
Objects can be created by calls of the form
new("cher", name, chromosome, start, end, cellType, antibody,
maxLevel, score, probes, extras, ...)
.
name
:chromosome
:start
:integer
, region start position on the
chromosome, e.g. 34318900end
:integer
, region end position on the
chromosome, e.g. 34320100cellType
:character
vector describing the cell
type the ChIP chip experiment has been done on,
e.g. "HeLa" or "human"antibody
:character
vector describing the
antibody or characteristic for which fragments were supposedly
enriched in immuno-precipitation step,
e.g. "Suz12" for the protein Suz12maxLevel
:numeric
, maximal (smoothed) probe
level in the cher, e.g. 2.00score
:numeric
of a cher score, currently we
use the sum of smoothed probe levels (log fold changes),
e.g. 69.16probes
:character vector
of probe identifiers
of all probes with match positions in the cher
extras
:list
of further elements used to
annotate the cher
; examples of such that are used in
Ringo
are:
cher
is located upstream of,
e.g. the transcriptional start site of "ENST00000379158".
See relateChers
for details.cher
is located inside of cher
's middle position to
features, e.g. TSSs of features upstream and inside; names
are the features to which the distances are given; only
meaningful in combination with typeUpstream
and
typeInside
; e.g. 55 with name "ENST00000379158"typeUpstream
; e.g. "Nudt2" typeInside
.update
method.cher
; see section
examples
belowchipAlongChrom
to plot the
cher
; see plot.cher
for more detailscher
,...); updates elements of the
cher
object; The further arguments in '...' are
interpreted. Arguments corresponding to defined slot names of the
cher
result in the value by that slot being replaced by the
specified value for the argument; argument names that do not
correspond to slot names of the object result in list elements of
the extras
list of the cher
being replaced by the
given values for these arguments or the values are appended to the
current extras
list and the argument names make up the list
names of the appended arguments. See section
examples
below for an example how to use this method.
A list in which each element is of class cher
, is called
a cherList
. This class, however, is rarely used (yet).
The cher
class used to be an S3 list before.
The term 'cher' is shorthand for 'ChIP-enriched region'. We think this term is more appropriate than the term 'peak' commonly used in ChIP-chip context. Within such regions the actual signal could show two or more actual signal peaks or none at all (long plateau).
Joern Toedling, Tammo Krueger
plot.cher
, findChersOnSmoothed
, relateChers
## how to create a cher object from scratch cherNudt2 <- new("cher", name="nudt2.cher", chromosome=9, start=34318954, end=34319944, antibody="Suz12", maxLevel=2.00, score=69.2, upSymbol="NUDT2") #extras=list(upSymbol="NUDT2")) cherNudt2 str(cherNudt2) ## use the update method (note:this update is biologically meaningless) cher2 <- update(cherNudt2, cellType="HeLa", downSymbol="P53", probes=c("probe1","probe2")) cher2; str(cher2) ## plot a cher object 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) plot(cherNudt2, smoothX, probeAnno=exProbeAnno, gff=exGFF, extent=5000)