naturalLog {ChIPanalyser} | R Documentation

## Accessor method the `naturalLog` slot in a `genomicProfileParameters` object.

### Description

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

### Usage

    naturalLog(object)

### Arguments

`object` | `object` is `genomicProfileParameters` 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 `genomicProfileParameters` object.

### Value

Returns the value assigned to the `naturalLog` slot in a `genomicProfileParameters` 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.

### Examples

    # Loading data
    data(ChIPanalyserData)
    #Loading PFM files
    PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
    #Building data objects
    GPP <- genomicProfileParameters(PFM=PFM,naturalLog=TRUE)
    #Setting new Value for naturalLog
    naturalLog(GPP)

[Package ChIPanalyser version 1.2.0 Index]