pics {PICS} | R Documentation

## Estimation of binding site positions

### Description

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

### Usage

    PICS(segReadsList,dataType=NULL, paraEM=NULL, paraPrior=NULL, nCores=1)

### Arguments

`segReadsList` | This object contains segmentation of Genome
`dataType` | The type of data you are processing: specified ‘TF’ for transcription factor.
`paraEM` | A list of parameters for the EM algorithm as returned by the `setParaEm` function. The default parameters should be good enough for most usages.

  `minK`: an `integer`, default=1. The minimum number of binding events per region. If the value is 0, the minimum number is automatically calculated.

  `maxK`: an `integer`, default=15. 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="BIC"

  `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 as returned by the `setParaPrior` function. The default parameters should be good enough for most usages.

  `xi`: an `integer`, default=200. The average DNA fragment size.

  `rho`: an `integer`, default=1. A variance parameter for the average DNA fragment size distribution.

  `alpha`: an `integer`, default=20. First hyperparameter of the inverse Gamma distribution for sigma^2 in the PICS model

  `beta`: an `integer`, default=40000. Second hyperparameter of the inverse Gamma distribution for sigma^2 in the PING model

  `lambda`: an `integer`, default=0. The precision of the prior for mu used for histone data.

  `dMu`: an `integer`, default=0. Our best guess for the distance between two neighboring nucleosomes.

`nCores` | An `integer`. The number of cores that should be used in parallel by the function.

### Methods

code

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

plot

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

sigmaSqR

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

sigmaSqF

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

score

  `signature(x = ``pics'')`: return the score for each binding event.

scoreF

  `signature(x = ``pics'')`: return the score of the forward (F) for each binding event.

scoreR

  `signature(x = ``pics'')`: return the score of the forward (R) for each binding event.

maxRange

  `signature(x = ``pics'')`: return the range maximum.

minRange

  `signature(x = ``pics'')`: return the range minimal.

K

  `signature(x = ``pics'')`: subset PICS object.

wigDensity

  `signature(x = ``pics'')`: return the density for each binding event.

### Author(s)

Xuekui Zhang, Arnaud Droit <arnaud.droit@crchuq.ualaval.ca> and Raphael Gottardo <rgottard@fhcrc.org>

### References

X. Zhang, G. Robertson, M. Krzywinski, K. Ning, A. Droit, S. Jones, and R. Gottardo, “PICS: Probabilistic Inference for ChIP-seq” arXiv, 0903.3206, 2009. To appear in Biometrics.

### See Also

`pics`

[Package PICS version 2.26.0 Index]