setParaPrior {PICS} | R Documentation

## List of parameters that can be used as an argument of PICS.

### Description

This function takes from 0 to 6 parameters as argument, check if they are valid and returns a list to be used in a call to PICS.

### Usage

    setParaPrior(
      xi = 200,
      rho = 1,
      alpha = 20,
      beta = 40000,
      lambda = 0,
      dMu = 0,
      dataType = NULL,
      PExi = 0
    )

### Arguments

`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 PICS model.
`lambda` | An `integer`. The precision of the prior for mu used for histone data.
`dMu` | An `integer`. Our best guess for the distance between two neighboring nucleosomes.
`dataType` | A character string. If a valid dataType is specified, use our suggested parameters. "MNase" or "sonicated"
`PExi` | A `numeric`. With paired end data, ‘xi’ can be calculated directly from the reads. If PExi is set, it will overwrite the xi determined by the dataType.

### Value

A `list` of 6 parameters to be used in `PICS`.

### See Also

setParaEM PICS

### Examples

    # set prior for PICS data
    paraPrior <- setParaPrior()
    # set prior for sonicated data using our selected default parameters
    paraPrior <- setParaPrior(dataType="sonicated")

[Package PICS version 2.38.0 Index]