chipSmooth {ChIPanalyser} | R Documentation

## Accessor methods for `chipSmooth` slot in a `occupancyProfileParameters` object.

### Description

Access or Extract `chipSmooth` slot in a `occupancyProfileParameters` object.

### Usage

    chipSmooth(object)

### Arguments

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

### 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 the `chipSmooth` slot in an `occupancyProfileParameters` 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 <- occupancyProfileParameters()
    # Accessing chipSd slot
    chipSmooth(OPP)

[Package ChIPanalyser version 1.2.0 Index]