backgroundSignal<- {ChIPanalyser} | R Documentation

## Setter method for `backgroundSignal` slot in a `parameterOptions`

### Description

Setter method for `backgroundSignal` slot in a `parameterOptions`

### Usage

    backgroundSignal(object)<-value

### Arguments

`object` | `object` is an `parameterOptions` object.
`value` | `value` is the value to be assigned to the `backgroundSignal` slot in `parameterOptions`. `backgroundSignal` should be a positive value. Defualt value is 0.

### Details

Defualt 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 to 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 `parameterOptions` object with a new `value` assigned to the `backgroundSignal` slot.

### 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()
    # Setting new value for backgroundSignal
    backgroundSignal(OPP) <- 0.2
    # Viewing whole object with new updated value
    OPP
    #Viewing single value in object
    backgroundSignal(OPP)

[Package ChIPanalyser version 1.9.1 Index]