naturalLog: Accessor method the 'naturalLog' slot in a 'parameterOptions'...
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

naturalLog

R Documentation

Accessor method the `naturalLog` slot in a `parameterOptions` object.

Description

Accessor method the naturalLog slot in a parameterOptions object.

Usage

naturalLog(object)

Arguments

object

object is parameterOptions object.

Details

During the computation of a Postion Weight Matrix, the Position Probability Matrix (derived from a Position Frequency Matrix) is log transformed. This parameter provides whcih "log transform" will be used. If TRUE, the Natural Log will bu used (ln). If FALSE, log2 will be used. We strongly encourage to set values when building a parameterOptions object.

Value

Returns the value assigned to the naturalLog slot in a parameterOptions object.

Author(s)

Patrick C.N. Martin <p.martin@essex.ac.uk>

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

# Loading data
data(ChIPanalyserData)

#Building data objects
GPP <- parameterOptions(naturalLog=TRUE)
#Setting new Value for naturalLog
naturalLog(GPP)

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