noiseFilter: Accessor Method for the 'noiseFilter' slot in a...
In patrickCNMartin/ChIPanalyserDev: ChIPanalyser: Predicting Transcription Factor Binding Sites
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
Accessor Method for the noiseFilter slot in a
parameterOptions object
Usage
1
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 <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
1
2
3
4
5
6
7
# Loading data
data(ChIPanalyserData)
#Building data objects
GPP <- parameterOptions(noiseFilter="sigmoid")
#Setting new Value for noiseFilter
noiseFilter(GPP)
patrickCNMartin/ChIPanalyserDev documentation built on Nov. 14, 2019, 4:39 p.m.
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Description Usage Arguments Details Value Author(s) References Examples
Description
Accessor Method for the noiseFilter slot in a
parameterOptions object
Usage
1 | noiseFilter(object)
|
Arguments
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 <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
1 2 3 4 5 6 7 | # Loading data
data(ChIPanalyserData)
#Building data objects
GPP <- parameterOptions(noiseFilter="sigmoid")
#Setting new Value for noiseFilter
noiseFilter(GPP)
|
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