Description Arguments Accessors Constructor Methods Methods Constructor Author(s) References See Also Examples

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.

`object` |
An object of class |

The PING package provide accessors to directly access to most of the parameters/standard errors and chromosomes. In the code snippets below, 'x' is a 'pingList' object. For all accessors, the 'pingError' objects are omitted, so that the accessors only return values for the 'ping' objects (i.e. all valid binding events).

- 'chromosome(x)'
Gets the chromosome names of all candidate regions.

- 'mu(x)'
Gets the position estimates of all binding sites identified in all candidate regions.

- 'delta(x)'
Gets the average fragment lengths of all binding sites identified in all candidate regions.

- 'sigmaSqF(x)'
Gets the F peak variances of all binding sites identified in all candidate regions.

- 'sigmaSqR(x)'
Gets the R peak variances of all binding sites identified in all candidate regions.

- 'seF(x)'
Gets the standard errors of all binding site position estimates identified in all candidate regions.

- 'seF(x)'
Gets the standard errors of all F peak modes identified in all candidate regions.

- 'seR(x)'
Gets the standard errors of all R peak modes identified in all candidate regions.

- 'score(x)'
Gets the scores of all binding events identified in all candidate regions.

newPingList(List, paraEM, paraPrior, minReads, N, Nc)

- List
The mixture weights (a vector)

- paraEM
The binding site positions (a vector)

- paraPrior
The DNA fragment lengths (a vector)

- N
The variance parameters for the forward distribution (vector)

- Nc
The variance parameters for the forward distribution (vector)

- [
`signature(x = "ping")`

: subset PING object.

- length
`signature(x = "ping")`

: subset PING object.

- as.data.frame
`signature(x = "pingList")`

: Coerce a`pingList`

to a`data.frame`

.

newPingList<-function(List, paraEM, paraPrior, minReads, N, Nc) constructs a new 'pingList' object with the following arguments.

- newPingList
- 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 reverse distribution (vector)

- seMu
The standard errors for mu (vector)

- seMuF
The standard errors for muF (vector)

- seMuR
The standard errors for muR (vector)

- seMuR
The standard errors for muR (vector)

- score
The scores for each binding event (vector)

- Nmerged
The number of peaks that were 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" PlosONE, under review.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ```
# 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 'pingError' object.
w<-1
mu<-10000
delta<-150
sigmaSqF<-5000
sigmaSqR<-5000
seMu<-10
seMuF<-10
seMuR<-10
score<-5
Nmerged<-0
converge<-TRUE
infMat<-matrix(0)
chr<-"chr1"
range<-c(1000,2000)
# Contructor
#myPING1<-newPing(w,mu,delta,sigmaSqF,sigmaSqR,seMu,seMuF,seMuR,score,Nmerged,converge,infMat,as.integer(range),chr)
#myPING2<-newPing(w,mu+1000,delta,sigmaSqF,sigmaSqR,seMu,seMuF,seMuR,score,Nmerged,converge,infMat,as.integer(range),chr)
#minReads<-list(perPeak=2,perRegion=5)
#paraPrior<-list(xi=200,rho=1,alpha=20,beta=40000)
#paraEM<-list(minK=1,maxK=15,tol=10e-6,B=100)
#N<-100
#Nc<-200
#mynewPingList<-newPingList(list(myPING1,myPING2), paraEM, paraPrior, minReads, as.integer(100), as.integer(200))
# Accessors
# Get the standard error of Mu
#se(mynewPingList)
# Get the standard error of MuF
#seF(mynewPingList)
# Get the scores
#score(mynewPingList)
``` |

PING documentation built on Nov. 17, 2017, 9:23 a.m.

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