chipSmooth<- {ChIPanalyser} | R Documentation

## Setter method for `chipSmooth` slot in `occupancyProfileParameters` object.

### Description

Setter method for `chipSmooth` slot in `occupancyProfileParameters` object.

### Usage

    chipSmooth(object) <- value

### Arguments

`object` | `object` is a `occupancyProfileParameters` object.
`value` | `value` is the positive numeric value to be assigned to the `chipSmooth` slot in `occupancyProfileParameters` Default value is 250 base pairs.

### Details

When computing ChIP-seq like (`computeChipProfile`) profile from occupancy data (see `computeOccupancy`), the profiles are smoothed using a window of a given size. The default value is set at 250 base pairs.If `chipSmooth` is set to 0 then the profile will not be smoothed. We strongly encourage to set values when building a `occupancyProfileParameters` object.

### Value

Returns a `occupancyProfileParameters` object with an updated value for `chipSmooth` 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 <- occupancyProfileParameters()
    # Setting new value for chipSd slot
    chipSmooth(OPP) <-  250

[Package ChIPanalyser version 1.2.0 Index]