occupancyProfileParameters {ChIPanalyser} | R Documentation

## Occupancy Profile Parameters

### Description

`occupancyProfileParameters` is a parameter storage object. Similarly to `genomicProfileParameters`, this object serves the purpose of handling the set of parameters needed when using certain functions.

### Usage

    occupancyProfileParameters(ploidy = 2 , boundMolecules = 1000 ,
        backgroundSignal = 0 ,  maxSignal = 1 , chipMean = 150 ,
        chipSd = 150 , chipSmooth = 250 , stepSize = 10 ,
        removeBackground = 0 , thetaThreshold = 0.1 )

### Arguments

`ploidy` | `ploidy`: A numeric Value descibing the ploidy of the organism. Default: 2
`boundMolecules` | `boundMolecules`: A vector (or single value) containing the number of bound Molecules (bound Transcription Factors): Default: 1000
`backgroundSignal` | `backgroundSignal`: A numeric value descibing the ChIP-seq background Signal (average signal from real ChIP seq data). Default: 0
`maxSignal` | `maxSignal`: A numeric value describing the highest ChIP-seq signal (from real ChIP-seq data). Default: 1
`chipMean` | `chipMean`: A numeric value describing the mean width of a ChIP- seq peak: Default:150
`chipSd` | `chipSd`: A numeric value describing the standard deviation of ChIP-seq peaks. Default: 150
`chipSmooth` | `chipSmooth`: A numeric value describing the width of the window used to smooth Occupancy profiles into ChIP profiles. Default:250
`stepSize` | `stepSize`: A numeric value describing the step Size (in base pairs) between each ChIP-seq score. Default:10 (Scored every 10 base pairs)
`removeBackground` | `removeBackground`: A numeric value describing the value at which score should be removed. Defualt:0 (If negative scores then remove)
`thetaThreshold` | `thetaThreshold`: A numeric value describing a threshold at which low ratios of correlation over Mean Squared Error (for accuracy estimation) should be removed. Default: 0.1

### Details

The purpose of this `occupancyProfileParameters` object is to store paramters used duing certin of the functions available in `ChIPanalyser`. As opposed to `genomicProfileParameters`, this object is not required for a function to run as all paramters have default values ( the object will be created internally as default values will be used - This also means that no argument is required for this object to be built). However, it is strongly advised to set these parameters to increase the goodness of fit between the predicted Profiles and the real ChIP-seq profiles. As an example, `maxSignal` is the maximum signal of the real ChIP-seq data, this signal will depend on the data being used thus should be tuned to opimise the model.

Default values are set at:

ploidy = 2

boundMolecules = 1000

backgroundSignal = 0

maxSignal = 1

chipMean = 150

chipSd = 150

chipSmooth = 250

stepSize = 10

removeBackground = 0

thetaThreshold = 0.1

### Value

Returns a `occupancyProfileParameters` 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.

### See Also

`occupancyProfileParameters-class` `genomicProfileParameters` `genomicProfileParameters-class`

### Examples

    OPP <- occupancyProfileParameters()
    # OR
    OPP <- occupancyProfileParameters(ploidy=2,
        boundMolecules=5000,backgroundSignal=0)

[Package ChIPanalyser version 1.2.0 Index]