mergeWindow {mixer}R Documentation

merge identified windows (peaks)

Description

Grouping identified windows with significant scores into non-overlapped peak regions

Usage

mergeWindow(windowX, wl, probeX, pl, radius, lambda=1/500, 
 window.cut=0.05, probe.cut.type = "lfdr", probe.cut=0.1, n.probe=3)

Arguments

windowX window level score. Output of funciton win
wl local FDR for winodw level score, output of fucntion lfdr
probeX probe level signal
pl local FDR for probe level signal, output of fucntion lfdr
radius half of the window size
lambda incident rate in the Poisson point process modeling the sonicantion process. If on average, there is one break up of DNA sequence per 500 bp, lambda = 1/500.
window.cut cutoff of window level local FDR
probe.cut.type if probe.cut.type="lfdr", use lfdr as probe level cutoff, otherwise use probe signal as cutoff
probe.cut cutoff of probe level local FDR
n.probe claim on window as a peak if at least n.probe in one window has local FDR smaler than probe.cut

Details

it is not precisly "merge". We simply pick up one significant peak and eliminate related probes and then re-evaluate window level score and pick up another peak if there is one.

Value

data.frame, each row for one peak

start start position of the peak
end end position of the peak
score score of the peak
n.probe the total number of probes in one peak
lfdr local FDR

Author(s)

Wei Sun

See Also

win


[Package mixer version 1.01 Index]