Description Usage Arguments Value Note Author(s) References See Also

Post process Estimation of binding site positions obtained from PING. Refit mixture models with stronger prior in candidate regions contain potential problems, and then convert final result into dataframe.

1 |

`ping` |
A 'pingList' object containing estimation of nuclesome positions, result of 'PING' function. |

`seg` |
An object of class 'segmentReadsList' containing the results for all regions pre-processed, 'segmentReads' function. |

`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`

. The average DNA fragment size.`rho`

:An

`integer`

. A variance parameter for the average DNA fragment size distribution.`alpha`

:An

`integer`

. First hyperparameter of the inverse Gamma distribution for sigma^2 in the PICS model`beta`

:An

`integer`

. Second hyperparameter of the inverse Gamma distribution for sigma^2 in the PING model`lambda`

:An

`integer`

. The lambda control Gaussian Markov Random Field prior on the distance of adjacent nucleosomes, we do not recommend user change the default value.`dMu`

:An

`integer`

. Our best guess for the distance between two neighboring nucleosomes.

`rho2, sigmaB2, alpha2, beta2` |
Integer values, the parameters in the prior of mixture models to be re-fitted. |

`min.dist` |
The minimum distance of two adjacent nucleosomes predicted from different candidate regions, smaller than that will be treated as duplicated predictions for the same nucleosomes. |

`score` |
A |

`dataType` |
A character string that can be set to use selected default parameters for the algorithm. |

`nCores` |
An |

`makePlot` |
A |

`FragmentLength, mart, seg.boundary, DupBound, IP, datname` |
Plotting parameters and options. |

`IP`

:A

`GRanges`

object. The reads used in segmentation process.`FragmentLength`

:An

`integer`

. The length of XSET profile extension

A `data.frame`

containing the estimation of binding site positions.

Based on our experiemt on a few real data sets, we suggestion to use following values of parameters. For sonication data we use rho1=1.2; sigmaB2=6400;rho=15;alpha1=10; alpha2=98; beta2=200000. For MNase data we use rho1=3; sigmaB2=4900; rho=8; alpha1=20; alpha2=100; beta2=100000. The value of xi depends on specy of sample, since that affect the length of linker-DNA. For example, we use xi=160 for yeast and xi=200 for mouse.

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.

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