backgroundSignal {ChIPanalyser} | R Documentation

## Accessor method for the `backgroundSignal` slot in a `parameterOptions` object.

### Description

Extract or access the `backgroundSignal` slot in a `parameterOptions` object.

### Usage

    backgroundSignal(object)

### Arguments

`object` | `object` is an `parameterOptions`

### Details

Default Value: 0

When computing `computeOccupancy`, a ChIP-seq background signal is used to scale Occupancy by considering both a `backgroundSignal` and a `maxSignal`. The `backgroundSignal` is also used to nomalise occupancies against maxOccupancy. The `backgroundSignal` usually comes from experimental data and is provided by user. As a general rule, if ChIP-seq data is available and will be used in `computeChIPProfile` , `profileAccuracyEstimate` or `plotOccupancyProfile`, it is advised to use the `backgroundSignal` from this data. We strongly encourage to set values when building a `parameterOptions` object.

### Value

Returns a `backgroundSignal` of a `parameterOptions` 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

    # Building occupancyProfileParameters object
    OPP <- parameterOptions()
    #Viewing single value in object
    backgroundSignal(OPP)

[Package ChIPanalyser version 1.12.0 Index]