setParaPrior {PICS} | R Documentation

## Function that returns a 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

Returns a list of 6 parameters to be used in PICS.

### Author(s)

Renan Sauteraud

### See Also

`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 2.28.0 Index]