chipMean<- {ChIPanalyser} | R Documentation

## Access methods for `chipMean` slot in `occupancyProfileParameters` object.

### Description

Access methods for `chipMean` slot in `occupancyProfileParameters` object.

### Usage

    chipMean(object)<-value

### Arguments

`object` | `object` is a `occupancyProfileParameters` object.
`value` | `value` is a positive numeric value that will be assigned to the `chipMean` slot. `chipMean` describes the average size of a ChIP-seq peak in base pairs.

### 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 `occupancyProfileParameters` object.

### Value

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

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 occupancyProfileParameters object
    OPP <- occupancyProfileParameters()
    # Setting new value for slot
    chipMean(OPP) <- 250

[Package ChIPanalyser version 1.2.0 Index]