newCher {Ringo} | R Documentation

## Create a list object of class cher

### Description

This is just a simple convenience function to create a `list` of class `cher` (ChIP-enriched region).

### Usage

    newCher(name, chr, start, end, cellType = NULL, antibody, maxLevel, score = NULL, probes = c(), ...)

### Arguments

`name` | character; (if possible) unique identifier for the cher
`chr` | character; chromosome the cher is located on
`start` | integer; genomic start coordinate of the Cher
`end` | integer; genomic end coordinate of the Cher
`cellType` | optional character describing the cell type in which the cher was identified.
`antibody` | required character vector describing the antibody or other characteristic for which fragments were supposedly enriched in immuno-precipitation step
`maxLevel` | numeric; maximal probe level in the cher
`score` | optional numeric score of the cher
`probes` | optional character vector of probe identifiers of probes that make up the cher
`...` | further arguments that will be additional elements of the `cher` list object

### Value

a list object of class `cher`, see `cher-class`

### Note

this function is called by other Ringo functions, such as `findChersOnSmoothed` and normally need not be called by the user.

### Author(s)

Tammo Krueger, Joern Toedling

### See Also

`cher-class`, `findChersOnSmoothed`

### Examples

      cher1 <- newCher("Suz12.Nudt2.upstream.cher",
                         chr="9", start=34318900, end=34320100,
                         antibody="Suz12",cellType="human",
                         maxLevel=2, score=99)
      print(cher1)

[Package Ringo version 1.56.0 Index]