naturalLog: Accessor method the 'naturalLog' slot in a 'parameterOptions'...
In patrickCNMartin/ChIPanalyserDev: ChIPanalyser: Predicting Transcription Factor Binding Sites
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
Accessor method the naturalLog slot in a
parameterOptions object.
Usage
1
naturalLog(object)
Arguments
object
object is parameterOptions object.
Details
During the computation of a Postion Weight Matrix, the
Position Probability Matrix (derived from a Position Frequency Matrix)
is log transformed. This parameter provides whcih "log transform" will be used.
If TRUE, the Natural Log will bu used (ln). If FALSE, log2 will be used.
We strongly encourage to set values when building a
parameterOptions object.
Value
Returns the value assigned to the naturalLog 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(naturalLog=TRUE)
#Setting new Value for naturalLog
naturalLog(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 the naturalLog slot in a
parameterOptions object.
Usage
1 | naturalLog(object)
|
Arguments
object |
|
Details
During the computation of a Postion Weight Matrix, the
Position Probability Matrix (derived from a Position Frequency Matrix)
is log transformed. This parameter provides whcih "log transform" will be used.
If TRUE, the Natural Log will bu used (ln). If FALSE, log2 will be used.
We strongly encourage to set values when building a
parameterOptions object.
Value
Returns the value assigned to the naturalLog 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(naturalLog=TRUE)
#Setting new Value for naturalLog
naturalLog(GPP)
|
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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