Usage
postPING(ping, seg, rho2=NULL, sigmaB2=NULL, alpha2=NULL, beta2=NULL, min.dist= 100, paraEM=NULL, paraPrior=NULL, score=0.05, dataType="MNase", nCores=1, makePlot=FALSE, FragmentLength=100, mart=NULL, seg.boundary=NULL, DupBound=NULL, IP=NULL, datname="")
Arguments
ping
A 'pingList' object containing estimation of nuclesome positions, result of 'PING' function.
seg
An object of class 'segmentReadsList' containing the results for all regions pre-processed, 'segmentReads' function.
paraEM
A list of parameters for the EM algorithm. The default parameters should be good enough for most usages.
paraPrior
A list of parameters for the prior distribution. The default parameters should be good enough for most usages.
rho2, sigmaB2, alpha2, beta2
Integer values, the parameters in the prior of mixture models to be re-fitted.
min.dist
The minimum distance of two adjacent nucleosomes predicted from different candidate regions, smaller than that will be treated as duplicated predictions for the same nucleosomes.
score
A numeric. The score threshold used when calling FilterPING.
dataType
A character string that can be set to use selected default parameters for the algorithm.
nCores
An integer. The number of cores that should be used in parallel by the function.
makePlot
A logical. Plot a summary of the output.
FragmentLength, mart, seg.boundary, DupBound, IP, datname
Plotting parameters and options.