stepSize_-: Setter Method for the 'stepSize' slot in a 'parameterOptions'

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

Setter Method for the stepSize slot in a parameterOptions

Description

Setter Method for the stepSize slot in a parameterOptions

Usage

stepSize(object) <- value

Arguments

object	object is a parameterOptions object
value	value is a positive numeric value that will be assigned to the stepSize slot in a parameterOptions object. Default is set at 10 base pairs.

Details

It possible to restrict the size of the ChIP-seq-like profile produced by computeChIPProfile. Instead of returning ChIP-seq like score for each base pair, it is possible to skip base pairs and only return the predicted enrichement score for every "n" base pair (n is the value assigned to stepSize). This will reduce the size of the output data (unless step size is very large, this will not affect the accuracy of the model). Default is set at 10 base pairs.

Value

Returns a parameterOptions object with an updated value for the stepSize slot.

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 Value for maxSignal
stepSize(OPP) <- 20

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