win {mixer}R Documentation

calculate window-level score

Description

calculate window-level scores based on probe-level score and probe-level local FDR.

Usage

win(chr, pL, pR, x, plfdr, lambda=1/500, radius=200, 
 precision=0.01)

Arguments

chr a vector, indicating chromosome of each probe
pL a vector of probe start positions
pR a vector of probe end positions
x probe signal
plfdr a list of class "lfdr", output of function lfdr
lambda the incident rate used to model the sonicaiton process, suppose there is one cut of DNA seqeunce per k bp, then lambda = 1/k
radius half of the window size
precision because the non-parametric methos is used, local FDR is estimated at fixed points, precision is the gap between adjacent points where local FDR are estimated. Currently, precision can only be one of 0.01 (default), 0.001, or 0.0001.

Details

each window is centered on one probe, and extedn length of raduis

Value

data.frame

start porbe start
end porbe end
wL number of probes to the left
wR number of probes to the right
x window-level score

Author(s)

Wei Sun

See Also

mergeWindow


[Package mixer version 1.03 Index]