This track actually creates two tracks: it displays the position of the predicted nucleosomes as well as the standard error associated with each prediction and an histogram of the score.
This object is used to gather all parameters from fitting PING to a single candidate region. The objet contains the following slots: 'estimates', 'infMat', 'Nmerged', 'converge', 'chr'. 'estimates' is a list containing all parameters estimates as well as standard errors. 'infMat' is the Cholesky decomposition of the information matrix, 'converge' is a logical value indicating whether the EM algorithm has converged, while 'chr' is a character string corresponding to a candidate region's chromosome. 'Nmerged' gives the number of binding events that were merged; binding events that overlap are merged (see the cited paper below for details).
This object is used to return an error code when the PING function failed to return a valid set of estimates for a candidate regions. This could be due to non-convergence of the EM algorithm, a singular information matrix, or a number of reads below the limit specified by the user. All of these are typically due to too few reads in the region and do not affect the rest of the analysis, as such regions would most likely be labelled as false positives.
This object is used to gather all parameters from fitting PING to multiple candidate regions (as returned by the 'segmentReads' function). The objet contains the following slots: 'List', 'paraPrior', 'paraEM', 'minReads', 'N', 'Nc'. 'List' is a list of 'ping' or 'pingError' objects. 'paraPrior' is a list containing the hyperparameters used for the prior, 'paraEM' is a list of convergence parameters for the EM, 'minReads' is a list containing the minimum number of reads used to fit a region with 'PING', 'N' is the total number of reads in the ChIP samples while 'Nc' is the total number of reads in the control sample.
postPING
(Package: PING) :
Post process Estimation of binding site positions obtained from PING
Post process Estimation of binding site positions obtained from PING. Refit mixture models with stronger prior in candidate regions contain potential problems, and then convert final result into dataframe.
providing 
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