newCER: Create a list object of class cher

In Ringo: R Investigation of ChIP-chip Oligoarrays

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)

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.