ping {PING} | R Documentation

## Estimation of binding site positions

### Description

This object contains Estimation of binding site positions and has the following slots: segReadsList.

### Usage

    PING(segReadsList, paraEM=NULL, paraPrior=NULL, dataType="MNase", detail=0, rescale=1, nCores=1)

### Arguments

`segReadsList` | This object contains segmentation of Genome
`paraEM` | A list of parameters for the EM algorithm. The default parameters should be good enough for most usages.

  `minK`: an `integer`, default=0. The minimum number of binding events per region. If the value is 0, the minimum number is automatically calculated.

  `maxK`: an `integer`, default=0. The maximum number of binding events per region. If the value is 0, the maximum number is automatically calculated.

  `tol`: a `numeric`, default=1e-4. The tolerance for the EM algorithm.

  `B`: an `integer`, default=100. The maximum number of iterations to be used.

  `mSelect`: a character string specifying the information criteria to be used when selecting the number of binding events. Default="AIC3"

  `mergePeaks`: a `logical` stating whether overlapping binding events should be picked. Default=TRUE

  `mapCorrect`: a `logical` stating whether mappability profiles should be incorporated in the estimation, i.e: missing reads estimated. Default=TRUE

`paraPrior` | A list of parameters for the prior distribution. The default parameters should be good enough for most usages.

  `xi`: an `integer`, default=150. The average DNA fragment size.

  `rho`: an `integer`, default=1.2. A variance parameter for the average DNA fragment size distribution.

  `alpha`: an `integer`, default=10. First hyperparameter of the inverse Gamma distribution for sigma^2 in the PICS model

  `beta`: an `integer`, default=20000. Second hyperparameter of the inverse Gamma distribution for sigma^2 in the PING model

  `lambda`: an `integer`, default=0.000064. The precision of the prior for mu used for histone data.

  `dMu`: an `integer`, default=200. Our best guess for the distance between two neighboring nucleosomes.

`dataType` | A character string that can be set to use selected default parameters for the algorithm.
`detail` | An `integer`. Additional information are printed if set to a value > 0.
`rescale` | An `integer`.
`nCores` | An `integer`. The number of cores that should be used in parallel by the function.

### Methods

code

  `signature(x = "ping")`: return the error code for each list element (i.e. candidate region) of a PING object. If the string is empty, there were no errors.

plot

  `signature(x = "ping")`: Plot all regions in the PING object. This might be long, and should only be used to plot a few regions, so subset the object before plotting.

sigmaSqR

  `signature(x = "ping")`: return the variance parameter of the reverse (R) distribution for each binding event.

sigmaSqF

  `signature(x = "ping")`: return the variance parameter of the forward (F) distribution for each binding event.

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.

maxRange

  `signature(x = "ping")`: return the range maximum.

minRange

  `signature(x = "ping")`: return the range minimal.

K

  `signature(x = "ping")`: subset PING object.

density

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

### Author(s)

Xuekui Zhang, ubcxzhang@gmail.com and Raphael Gottardo, raphael.gottardo@ircm.qc.ca Sangsoon Woo, swoo@fhcrc.org

### See Also

`ping`

[Package PING version 2.30.0 Index]