boundMolecules_-: Setter method for the 'boundMolecules' slot in a...

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Setter method for the boundMolecules slot in a parameterOptions object.

Description

Setter method for the boundMolecules slot in a parameterOptions object.

Usage

boundMolecules(object)<-value

Arguments

object	object is a parameterOptions object.
value	value is a positive integer or vector of positive integers describing the number ofmolecules bound to DNA. Defaut value is 1000.

Details

Default value: 1000 When computing occupancy (computeOccupancy), a value for the number of bound Molecules to DNA is needed. This value can be updated and set in a parameterOptions object. If the number of molecules is unknown, it is possible to infer this value with computeOptimal. We strongly encourage to set values when building a parameterOptions object.

Value

Returns a parameterOptions object with an updated value for boundMolecules.

Author(s)

Patrick C.N. Martin <[e-mail]>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

Examples

# Building parameterOptions object
OPP <- parameterOptions()
# Setting new boundMolecules value in OPP
boundMolecules(OPP) <- 5000
#Checking value in whole object
OPP
#Checking single value by slot accessor
boundMolecules(OPP)

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.