defaultControl: Default parameters for simChIP
In ChIPsim: Simulation of ChIP-seq experiments

Description Usage Arguments Details Value Author(s) See Also Examples

Produces a list of parameters for each of the functions used to carry out the various stages of the simulation.

1 2	defaultControl(features = list(), bindDensity = list(), readDensity = list(), readNames = list(), readSequence = list())

`features`	Parameters for feature generation.
`bindDensity`	Parameters for the conversion of feature sequence into binding site densities.
`readDensity`	Parameters for the conversion of binding site densities into read densities. Always provides parameters `fragment` Default: `fragDens` `meanLength` Default: 160
`readNames`	Parameters for the generation of read names.
`readSequence`	Parameters for the conversion of read positions into read sequences. Always provides parameters `qualityFun` `readQualitySample` `errorFun` `readError` `readLen` 36

Any parameters passed as part of list to one of the arguments of defaultControl will be passed on to the corresponding function in simChIP. The build-in defaults can be overwritten by providing a list entry with the same name.

List of parameters for use as the control argument to simChIP.

Peter Humburg

defaultFunctions, simChIP