PICS (version 2.16.0)

setParaPrior: 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.

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")