ping-class {PING} | R Documentation |
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).
The PING package provide accessors to directly access to most of the parameters/standard errors and chromosome. In the code snippets below, 'x' is a 'ping' object.
Gets the chromosome name of the candidate region.
Gets the position estimates of all binding sites identified in the region.
Gets the average fragment lengths of all binding sites identified in the region.
Gets the F peak variances of all binding sites identified in the region.
Gets the R peak variances of all binding sites identified in the region.
Gets the standard errors of all binding site position estimates identified in the region.
Gets the standard errors of all F peak modes identified in the region.
Gets the standard errors of all R peak modes identified in the region.
signature(x = "ping")
: return the score for each binding event.
signature(x = "ping")
: return the score of the forward (F) for each binding event.
signature(x = "ping")
: return the score of the forward (R) for each binding event.
newPing(w,mu,delta,sigmaSqF,sigmaSqR,seMu,seMuF,seMuR,score,Nmerged,converge,infMat,chr) construct a new 'ping' object with the following arguments:
The mixture weights (a vector)
The binding site positions (a vector)
The DNA fragment lengths (a vector)
The variance parameters for the forward distribution (vector)
The variance parameters for the forward distribution (vector)
The standard errors for mu (vector)
The standard errors for muF (vector)
The standard errors for muR (vector)
The scores for each binding event (vector)
The number of peaks that got merged (integer)
A logical value, TRUE, if the EM as converged
The information matrix
The chromosome for the region
Xuekui Zhang <xzhang@stat.ubc.ca>, Sangsoon Woo, swoo@fhcrc.org and Raphael Gottardo <raphael.gottardo@ircm.qc.ca>
Xuekui Zhang, Gordon Robertson, Sangsoon Woo, Brad G. Hoffman, and Raphael Gottardo, "Probabilistic Inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data" GenomeBiology, under review.
# Here is an example of how to construct such a region. # Typically, you would not do this manually, you would use the ping function to return a 'pingList' # that contains a list of 'ping' or a 'pingError' object. w<-1 mu<-10000 delta<-150 sigmaSqF<-5000 sigmaSqR<-5000 seMu<-10 seMuF<-10 seMuR<-10 score<-5 Nmerged<-0 converge<-TRUE chr<-"chr1" range<-c(1000,2000) # Contructor #myPING<-newPing(w,mu,delta,sigmaSqF,sigmaSqR,seMu,seMuF,seMuR,score,Nmerged,as.integer(range),chr)