chipSmooth: Accessor methods for 'chipSmooth' slot in a...
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites
chipSmooth R Documentation
Accessor methods for chipSmooth slot in a
parameterOptions object.
Description
Access or Extract chipSmooth slot in a
parameterOptions object.
Usage
chipSmooth(object)
Arguments
object
object is a parameterOptions object.
Details
When computing ChIP-seq like (computeChIPProfile) profile
from occupancy data (see computeOccupancy),
the profiles are smoothed using a window of a given size.
The default value is set at 250 base pairs. If chipSmooth
is set to 0 then the profile will not be smoothed.
We strongly encourage to set values when building a
parameterOptions object.
Value
Returns the chipSmooth slot in an
parameterOptions object.
Author(s)
Patrick C.N. Martin <pcnmartin@gmail.com>
References
Zabet NR, Adryan B (2015) Estimating binding properties of transcription
factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.
Examples
# Building parameterOptions object
OPP <- parameterOptions()
# Accessing chipSd slot
chipSmooth(OPP)
patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.
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| chipSmooth | R Documentation |
Accessor methods for chipSmooth slot in a
parameterOptions object.
Description
Access or Extract chipSmooth slot in a
parameterOptions object.
Usage
chipSmooth(object)
Arguments
object |
|
Details
When computing ChIP-seq like (computeChIPProfile) profile
from occupancy data (see computeOccupancy),
the profiles are smoothed using a window of a given size.
The default value is set at 250 base pairs. If chipSmooth
is set to 0 then the profile will not be smoothed.
We strongly encourage to set values when building a
parameterOptions object.
Value
Returns the chipSmooth slot in an
parameterOptions object.
Author(s)
Patrick C.N. Martin <pcnmartin@gmail.com>
References
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.
Examples
# Building parameterOptions object
OPP <- parameterOptions()
# Accessing chipSd slot
chipSmooth(OPP)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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