chipSd<- {ChIPanalyser} | R Documentation

## Setter methods for `chipSd` slot in a `parameterOptions` object.

### Description

Setter methods for `chipSd` slot in a `parameterOptions` object.

### Usage

    chipSd(object)<-value

### Arguments

`object` | `object` is `parameterOptions` object.
`value` | `value` is a positive nurmeric value that will be assigned to `chipSd` slot. Default value is 150.

### 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 `parameterOptions` object.

### Value

Returns a `parameterOptions` 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 parameterOptions object
    OPP <- parameterOptions()
    # Setting new value for chipSd slot
    chipSd(OPP) <-  250

[Package ChIPanalyser version 1.16.0 Index]