Description Accessors Constructor Author(s) References See Also Examples

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.

- ‘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.

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

Xuekui Zhang <[email protected]>, Sangsoon Woo, [email protected] and Raphael Gottardo <[email protected]>

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
# 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)
``` |

PING documentation built on Nov. 1, 2018, 2:40 a.m.

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