ScalingFactorPWM {ChIPanalyser} | R Documentation

## Accessor method for the `lambda` slot in a `genomicProfileParameters` object

### Description

Accessor method for the `lambda` slot in a `genomicProfileParameters` object

### Usage

    ScalingFactorPWM(object)

### Arguments

`object` | `object` is a `genomicProfileParameters` object

### Details

The model used in `ChIPanalyser` relies on a scaling factor (scaling Transcription Factor binding affinity) for the PWM Score (or binding energy). It is also referred to as `lambda`. In the case a vector of values is provided, each value will be either computed individually ( as it will be the case in `computeGenomeWidePWMScore`) or in combination with `boundMolecules` (as it will be the case in `computeOccupancy`).

### Value

Returns the value or vector assigned to the `lambda` slot in a `genomicProfileParameters` object

### Author(s)

Patrick C. N. Martin <pm16057@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, ScalingFactorPWM=c(0.5,1,1.5))
    #Accessing value for ScalingFactorPWM
    ScalingFactorPWM(GPP)

[Package ChIPanalyser version 1.2.0 Index]