newPeak {Ringo}R Documentation

Create a list object of class peak

Description

This is just a simple convenience function to create a list of class peak.

Usage

newPeak(name, chr, start, end, cellType = NULL, modification, maxPeak, score = NULL, probes = c(), ...)

Arguments

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

Value

a list object of class peak, see peak-class

Note

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

Author(s)

Tammo Krueger, Joern Toedling

See Also

peak-class, findPeaksOnSmoothed

Examples

  my.peak <- newPeak("H3ac.HAND2.upstream.peak",
                     chr="8", start=60210400, end=60213000,
                     modification="H3ac",cellType="cellLine.HL1",
                     maxPeak=3.5, score=100)
  print(my.peak)

[Package Ringo version 1.0.0 Index]