boundMolecules<- {ChIPanalyser} | R Documentation

## Setter method for the `boundMolecules` slot in a `occupancyProfileParameters` object.

### Description

Setter method for the `boundMolecules` slot in a `occupancyProfileParameters` object.

### Usage

    boundMolecules(object)<-value

### Arguments

`object` | `object` is a `occupancyProfileParameters` object.
`value` | `value` is a positive integer or vector of positive integers describing the number ofmolecules bound to DNA. Defaut value is 1000.

### Details

Default value: 1000 When computing occupancy (`computeOccupancy`), a value for the number of bound Molecules to DNA is needed. This value can be updated and set in a `occupancyProfileParameters` object. If the number of molecules is unknown, it is possible to infer this value with `computeOptimal`. We strongly encourage to set values when building a `occupancyProfileParameters` object.

### Value

Returns a `occupancyProfileParameters` object with an updated value for `boundMolecules`.

### 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 boundMolecules value in OPP
    boundMolecules(OPP) <- 5000
    #Checking value in whole object
    OPP
    #Checking single value by slot accessor
    boundMolecules(OPP)

[Package ChIPanalyser version 1.2.0 Index]