defaultControl {ChIPsim}R Documentation

Default parameters for simChIP

Description

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

Usage

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

Arguments

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

Details

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.

Value

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

Author(s)

Peter Humburg

See Also

defaultFunctions, simChIP

Examples

defaultControl()
defaultControl(features=list(maxTail=0), readSequence=list(readLen=50))

[Package ChIPsim version 1.38.0 Index]