noiseFilter: Accessor Method for the 'noiseFilter' slot in a...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

Accessor Method for the noiseFilter slot in a parameterOptions object

1	noiseFilter(object)

object

object is parameterOptions object

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

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

Patrick C. N. Martin <p.martin@essex.ac.uk>

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84<e2><80><93>94.

# Loading data
data(ChIPanalyserData)

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