cher-class {Ringo} | R Documentation

## Class "cher" - ChIP-enriched region

### Description

An object of class `cher` (ChIP-enriched region) holds characteristics of an enriched genomic region from ChIP chip data.

### Objects from the Class

Objects can be created by calls of the form `new("cher", name, chromosome, start, end, cellType, antibody, maxLevel, score, probes, extras, ...)`.

### Slots

`name`:

  character vector of length 1 unequivocally describing the cher, e.g. "Suz12.Nudt2.upstream.cher"

`chromosome`:

  character vector of length one, naming the chromosome of the region, e.g. "9"

`start`:

  `integer`, region start position on the chromosome, e.g. 34318900

`end`:

  `integer`, region end position on the chromosome, e.g. 34320100

`cellType`:

  `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 Suz12

`maxLevel`:

  `numeric`, maximal (smoothed) probe level in the cher, e.g. 2.00

`score`:

  `numeric` of a cher score, currently we use the sum of smoothed probe levels (log fold changes), e.g. 69.16

`probes`:

  `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:

  typeUpstream

    optional character vector of features that this `cher` is located upstream of, e.g. the transcriptional start site of "ENST00000379158". See `relateChers` for details.

  typeInside

    optional character vector of features that this `cher` is located inside of

  distMid2TSS

    optional named numeric vector of distances of the `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"

  upSymbol

    optional character vector of gene symbols of features the cher is located upstream of; supplements `typeUpstream`; e.g. "Nudt2"

  inSymbol

    optional character vector of gene symbols of features the cher is located upstream of; supplements `typeInside`.

  ...

    further list elements can be added using the `update` method.

### Methods

initialize

  create a new `cher`; see section `examples` below

plot

  calls `chipAlongChrom` to plot the `cher`; see `plot.cher` for more details

update

  signature(`cher`,...); 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.

cellType

  obtain or replace the description of the cell type, the ChIP-enriched regions was found in with this antibody

probes

  obtain the vector of probes involved in a ChIP-enriched region

### cherList

A list in which each element is of class `cher`, is called a `cherList`. This class, however, is rarely used (yet).

### Note

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).

### Author(s)

Joern Toedling, Tammo Krueger

### See Also

`plot.cher`, `findChersOnSmoothed`, `relateChers`

### Examples

      ## 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)

[Package Ringo version 1.44.0 Index]