newCher

character; (if possible) unique identifier for the cher

name

character; chromosome the cher is located on

integer; genomic start coordinate of the Cher

start

integer; genomic end coordinate of the Cher

optional character describing the cell type in which
    the cher was identified.

cellType

required character vector describing the
    antibody or other characteristic for which fragments were supposedly
    enriched in immuno-precipitation step

antibody

maxLevel

score

optional character vector of probe identifiers of probes
  that make up the cher

probes

further arguments that will be additional elements of the
  <code>cher</code> list object


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


internal

The package Ringo facilitates the primary analysis
of ChIP-chip data. The main functionalities of the package are
data read-in, quality assessment, data visualisation and
identification of genomic regions showing enrichment in ChIP-chip.
The package has functions to deal with two-color oligonucleotide
microarrays from NimbleGen used in ChIP-chip projects, but also
contains more general functions for ChIP-chip data analysis, given
that the data is supplied as RGList (raw)  or ExpressionSet (pre-
processed).
The package employs functions from various other packages of the
Bioconductor project and provides additional ChIP-chip-specific
and NimbleGen-specific functionalities.

J Toedling

Ringo

R Investigation of ChIP-chip Oligoarrays

newCher function

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

newCher: Create a list object of class cher

Description

Usage

Arguments

Value

See Also

Examples