naturalLog_-: Setter method for the 'naturalLog' slot in a...
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

naturalLog<-

R Documentation

Setter method for the `naturalLog` slot in a `parameterOptions` object.

Description

Setter method for the naturalLog slot in a parameterOptions object.

Usage

naturalLog(object)<- value

Arguments

`object`	`object` is a `parameterOptions` object.
`value`	`value` is a logical value that will determine if the natural log or log2 should be used for the computation of the Position Weight Matrix.

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 parameterOptions object with an updated value for the naturalLog slot.

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
OPP <- parameterOptions(naturalLog=TRUE)
#Setting new Value for naturalLog
naturalLog(OPP) <- FALSE

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