ping-class {PING} | R Documentation

## 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

### Author(s)

Xuekui Zhang <xzhang@stat.ubc.ca>, Sangsoon Woo, swoo@fhcrc.org and Raphael Gottardo <raphael.gottardo@ircm.qc.ca>

### 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)

[Package PING version 2.26.0 Index]