setParaPrior: List of parameters that can be used as an argument of PICS.
In PICS: Probabilistic inference of ChIP-seq

Description Usage Arguments Value See Also Examples

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.

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

`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.

A list of 6 parameters to be used in PICS.

setParaEM PICS

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