occupancyProfileParameters-class {ChIPanalyser} | R Documentation

## Class `"occupancyProfileParameters"`

### 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.

### Objects from the Class

Objects can be created by calls of the form `occupancyProfileParameters(ploidy = 2 , boundMolecules = 1000 , backgroundSignal = 0 , maxSignal = 1 , chipMean = 150 , chipSd = 150 , chipSmooth = 250 , stepSize = 10 , removeBackground = 0 , thetaThreshold = 0.1 )`

### Slots

`ploidy`:

  Object of class `"numeric"`: A numeric Value descibing the ploidy of the organism. Default: 2

`boundMolecules`:

  Object of class `"vector"`: A vector (or single value) containing the number of bound Molecules (bound Transcription Factors): Default: 1000

`backgroundSignal`:

  Object of class `"numeric"`: A numeric value descibing the ChIP-seq background Signal (average signal from real ChIP seq data). Default: 0

`maxSignal`:

  Object of class `"numeric"`: A numeric value describing the highest ChIP-seq signal (from real ChIP-seq data). Default: 1

`chipMean`:

  Object of class `"numeric"`: A numeric value describing the mean width of a ChIP- seq peak. Default:150

`chipSd`:

  Object of class `"numeric"`: A numeric value describing the standard deviation of ChIP-seq peaks. Default: 150

`chipSmooth`:

  Object of class `"vector"`: A numeric value describing the width of the window used to smooth Occupancy profiles into ChIP profiles. Default:250

`stepSize`:

  Object of class `"numeric"`: A numeric value describing the step Size (in base pairs) between each ChIP-seq score. Default:10 (Scored every 10 base pairs)

`removeBackground`:

  Object of class `"numeric"`: A numeric value describing the value at which score should be removed. Defualt:0 (If negative scores then remove)

`thetaThreshold`:

  Object of class `"numeric"`: 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

### Methods

backgroundSignal<-

  `signature(object = "occupancyProfileParameters", value = "numeric")`: Slot Setter Method

backgroundSignal

  `signature(object = "occupancyProfileParameters")`: Slot Accessor Method

boundMolecules<-

  `signature(object = "occupancyProfileParameters", value = "vector")`: Slot Setter Method

boundMolecules

  `signature(object = "occupancyProfileParameters")`: Slot Accessor Method

chipMean<-

  `signature(object = "occupancyProfileParameters", value = "numeric")`: Slot Setter Method

chipMean

  `signature(object = "occupancyProfileParameters")`: Slot Accessor Method

chipSd<-

  `signature(object = "occupancyProfileParameters", value = "numeric")`: Slot Setter Method

chipSd

  `signature(object = "occupancyProfileParameters")`: Slot Accessor Method

chipSmooth<-

  `signature(object = "occupancyProfileParameters", value = "vector")`: Slot Setter Method

chipSmooth

  `signature(object = "occupancyProfileParameters")`:Slot Accessor Method

maxSignal<-

  `signature(object = "occupancyProfileParameters", value = "numeric")`: Slot Setter Method.

maxSignal

  `signature(object = "occupancyProfileParameters")`: Slot Accessor Method

ploidy<-

  `signature(object = "occupancyProfileParameters", value = "numeric")`: Slot Setter Method

ploidy

  `signature(object = "occupancyProfileParameters")`: Slot Accessor Method

removeBackground<-

  `signature(object = "occupancyProfileParameters", value = "vector")`:Slot Setter Method

removeBackground

  `signature(object = "occupancyProfileParameters")`: Slot Setter Method

show

  `signature(object = "occupancyProfileParameters")`: Slot Accessor Method

stepSize<-

  `signature(object = "occupancyProfileParameters", value = "numeric")`: Slot Setter Method

stepSize

  `signature(object = "occupancyProfileParameters")`: Slot Accessor Method

thetaThreshold<-

  `signature(object = "occupancyProfileParameters", value = "numeric")`: Slot Setter Method

thetaThreshold

  `signature(object = "occupancyProfileParameters")`: Slot Accessor Method

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

### Examples

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

[Package ChIPanalyser version 1.2.0 Index]