noiseFilter<- {ChIPanalyser} | R Documentation

## Setter Method for the `noiseFilter` slot in a `parameterOptions` object

### Description

Setter Method for the `noiseFilter` slot in a `parameterOptions` object

### Usage

    noiseFilter(object) <- value

### Arguments

`object` | `object` is `parameterOptions` object
`value` | `value` is the value to be assigned to the `noiseFilter` slot (zero - mean - median -sigmoid)

### Details

Noise filtering method that should be used on ChIP-seq data. Four methods are available: Zero, Mean, Median and Sigmoid. Zero removes all ChIP-seq scores bellow zero, mean under the mean score, median under median score and sigmoid assignes a weight to each score based on a logistic regression curve. Mid point is set at 95 95 quantile of ChIP-seq scores. Below midpoint will receive a score between 0 and 1 , everything above will receive a score between 1 and 2

### Value

Returns the value assigned to the `noiseFilter` slot in a `parameterOptions` object.

### Author(s)

Patrick C. N. Martin <p.martin@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

    # Loading data
    data(ChIPanalyserData)

    #Building data objects
    GPP <- parameterOptions(noiseFilter="sigmoid")
    #Setting new Value for noiseFilter
    noiseFilter(GPP) <-"zero"

[Package ChIPanalyser version 1.16.0 Index]