thetaThreshold {ChIPanalyser} | R Documentation

## Accessor method for the `thetaThreshold` slot in a `occupancyProfileParameters` object

### Description

Accessor method for the `thetaThreshold` slot in a `occupancyProfileParameters` object

### Usage

    thetaThreshold(object)

### Arguments

`object` | `object` is a `occupancyProfileParameters` object

### Details

In order to measure the accuracy of predicted models agaisnt real ChIP-seq data, `ChIPanalyser` uses three "measures": correlation, Mean Squared Error and Theta. Theta is an in house metric that can be described as a modified ratio of correlation over Mean Squarred Error. The higher the value of theta , the better the fit becomes. The theta threshold serves the purpose of avoiding extreme values and thus clarifying optimal parameter heat maps ( see `plotOptimalHeatMaps`). Default is set at 0.1

### Value

Returns the value assigned to the `thetaThreshold` slot in a `occupancyProfileParameters`

### 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

    # Building occupancyProfileParameters object
    OPP <- occupancyProfileParameters()
    #Setting new Value for thetaThreshold
    thetaThreshold(OPP)

[Package ChIPanalyser version 1.2.0 Index]