noiseFilter: Accessor Method for the 'noiseFilter' slot in a...

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Accessor Method for the noiseFilter slot in a parameterOptions object

Description

Accessor Method for the noiseFilter slot in a parameterOptions object

Usage

noiseFilter(object)

Arguments

object

object is parameterOptions object

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 <[e-mail]>

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)

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.