PING (version 2.16.0)

ping-class: The ping class

Description

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).

Accessors

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.

`chromosome(x)'

Gets the chromosome name of the candidate region.

`mu(x)'

Gets the position estimates of all binding sites identified in the region.

`delta(x)'

Gets the average fragment lengths of all binding sites identified in the region.

`sigmaSqF(x)'

Gets the F peak variances of all binding sites identified in the region.

`sigmaSqR(x)'

Gets the R peak variances of all binding sites identified in the region.

`se(x)'

Gets the standard errors of all binding site position estimates identified in the region.

`seF(x)'

Gets the standard errors of all F peak modes identified in the region.

`seR(x)'

Gets the standard errors of all R peak modes identified in the region.

score

signature(x = "ping"): return the score for each binding event.

scoreF

signature(x = "ping"): return the score of the forward (F) for each binding event.

scoreR

signature(x = "ping"): return the score of the forward (R) for each binding event.

Constructor

newPing(w,mu,delta,sigmaSqF,sigmaSqR,seMu,seMuF,seMuR,score,Nmerged,converge,infMat,chr) construct a new 'ping' object with the following arguments:

w

The mixture weights (a vector)

mu

The binding site positions (a vector)

delta

The DNA fragment lengths (a vector)

sigmaSqF

The variance parameters for the forward distribution (vector)

sigmaSqR

The variance parameters for the forward distribution (vector)

seMu

The standard errors for mu (vector)

seMuF

The standard errors for muF (vector)

seMuR

The standard errors for muR (vector)

score

The scores for each binding event (vector)

Nmerged

The number of peaks that got merged (integer)

converge

A logical value, TRUE, if the EM as converged

infMat

The information matrix

chr

The chromosome for the region

References

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.

See Also

ping pingError

Examples

# 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)