chipMean {ChIPanalyser} | R Documentation

## Accessor method for `chipMean` slot in a `parameterOptions` object.

### Description

Accessor method for `chipMean` slot in a `parameterOptions` object.

### Usage

    chipMean(object)

### Arguments

`object` | `object` is a `parameterOptions`

### Details

Default vlaue : 150 When computing ChIP-seq like profiles (`computeChIPProfile`, the occupancy values given by `computeOccupancy` are transformed into ChIP-seq like profiles. The average size of a ChIP-seq peak was described by Kaplan (Kaplan et al. , 2011). It is advised to use the average width of ChIP peaks from actual ChIP-seq data. We strongly encourage to set values when building a `parameterOptions` object.

### Value

Returns `chipMean` slot from 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.

Kaplan T.,Li X.-Y.,Sabo P.J.,Thomas S.,Stamatoyannopoulos J.A., Biggin M.D., EisenM.B. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development, PLoS Genet.,2011, vol. 7 pg. e1001290

### Examples

    # Building parameterOptions object
    OPP <- parameterOptions()
    #Accessing chipMean slot in OPP
    chipMean(OPP)

[Package ChIPanalyser version 1.9.1 Index]