newPeak {Ringo} | R Documentation |
This is just a simple convenience function to create a list
of class peak
.
newPeak(name, chr, start, end, cellType = NULL, modification, maxPeak, score = NULL, probes = c(), ...)
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 |
a list object of class peak
, see peak-class
this function is called by other Ringo functions, such as
findPeaksOnSmoothed
and normally need not be called by
the user.
Tammo Krueger, Joern Toedling
peak-class
, findPeaksOnSmoothed
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)