PWMThreshold: Accessor method for the 'PWMThreshold' 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 PWMThreshold slot in a
parameterOptions object
Usage
1
PWMThreshold(object)
Arguments
object
object is a parameterOptions object
Details
The computePWMScore function requires a so-called PWM Threshold.
This threshold represents the Threshold at which PWM Score should be selected.
The PWMThreshold is a positive numeric value (between 0 and 1.
If set at 0, all sites will be selected. If set at 0.7 (Default value),
then 70 % of PWM Score (and by extension binding sites) will be IGNORED.
The top 30 % will be selected.
Value
Returns the value assinged to the PWMThreshold slot in a
parameterOptions object
Author(s)
Patrick C. N. Martin <pm16057@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
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3
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5
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7
# Loading data
data(ChIPanalyserData)
#Building data objects
GPP <- parameterOptions(PWMThreshold=0.7)
#Accessing Value for PWMThreshold
PWMThreshold(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 PWMThreshold slot in a
parameterOptions object
Usage
1 | PWMThreshold(object)
|
Arguments
object |
|
Details
The computePWMScore function requires a so-called PWM Threshold.
This threshold represents the Threshold at which PWM Score should be selected.
The PWMThreshold is a positive numeric value (between 0 and 1.
If set at 0, all sites will be selected. If set at 0.7 (Default value),
then 70 % of PWM Score (and by extension binding sites) will be IGNORED.
The top 30 % will be selected.
Value
Returns the value assinged to the PWMThreshold slot in a
parameterOptions object
Author(s)
Patrick C. N. Martin <pm16057@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(PWMThreshold=0.7)
#Accessing Value for PWMThreshold
PWMThreshold(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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