naturalLog<- {ChIPanalyser} | 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.

### Examples

    # Loading data
    data(ChIPanalyserData)

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

[Package ChIPanalyser version 1.9.1 Index]