chipSd {ChIPanalyser} | R Documentation

## Accessor method for `chipSd` slot in a `occupancyProfileParameters` object.

### Description

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

### Usage

    chipSd(object)

### Arguments

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

### Details

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). The average peak size is subject to variation. This variation is accounted for with `chipSd`. It is advised to use the standard deviation of ChIP peak width 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 `chipSd`.

### 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., Eisen M.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()
    # Accessing chipSd slot
    chipSd(OPP)

[Package ChIPanalyser version 1.2.0 Index]