postPING {PING} | R Documentation

## Post process Estimation of binding site positions obtained from PING

### Description

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.

### Usage

    postPING(
      ping,
      seg,
      rho2 = NULL,
      sigmaB2 = NULL,
      alpha2 = NULL,
      beta2 = NULL,
      min.dist = 100,
      paraEM = NULL,
      paraPrior = NULL,
      score = 0.05,
      dataType = "MNase",
      nCores = 1,
      makePlot = FALSE,
      FragmentLength = 100,
      mart = NULL,
      seg.boundary = NULL,
      DupBound = NULL,
      IP = NULL,
      datname = ""
    )

### Arguments

`ping` | A `pingList` object containing estimation of nucleosome positions as returned by the `PING` function.
`seg` | An object of class `segmentReadsList` containing the results for all pre-processed regions as returned by `segmentReads`.
`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.
`paraEM` | A `list` of parameters for the EM algorithm. The default parameters should be good enough for most usages.
`paraPrior` | A `list` of parameters for the prior distribution. The default parameters should be good enough for most usages.
`score` | A `numeric`. The score threshold used when calling `FilterPING`.
`dataType` | A `character` that can be set to use selected default parameters for the algorithm.
`nCores` | An `integer`. The number of cores that should be used in parallel by the function.
`makePlot` | A `logical`. Plot a summary of the output.
`FragmentLength` | An `integer`. The length of XSET profile extension
`mart, seg.boundary, DupBound, datname` | Plotting parameters and options.
`IP` | A `GRanges` object. The reads used in segmentation process.
`minK` | An `integer`.The minimum number of binding events per region. If the value is 0, the minimum number is automatically calculated.
`maxK` | An `integer`. The maximum number of binding events per region. If the value is 0, the maximum number is automatically calculated.
`tol` | A `numeric`. The tolerance for the EM algorithm.
`B` | An `integer`. The maximum number of iterations to be used.
`mSelect` | A `character` 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.
`mapCorrect` | A `logical` stating whether mappability profiles should be incorporated in the estimation, i.e: missing reads estimated.
`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.

### Value

A `data.frame` containing the estimated binding site positions

### Note

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 specs of sample, since that affect the length of linker-DNA. For example, we use xi=160 for yeast and xi=200 for mouse.

### See Also

PING, plotSummary

[Package PING version 2.38.0 Index]