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 1.6.0 Index]