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

Description Usage Arguments Value See Also Examples

View source: R/setPara.R

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

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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

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

SRenan/PICS documentation built on Jan. 19, 2020, 5:59 a.m.