Create a list object of class cher

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Description

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

Usage

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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

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

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