strandRule: Accessor Method for the 'strandRule' 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 strandRule slot in a
parameterOptions object
Usage
1
strandRule(object)
Arguments
object
object is a parameterOptions object
Details
When computing the PWM Scores and if whichstrand
is set to "+-", strandRule will determine how to handle both strands
( one of three options : "mean", "max", "sum"). If set to "mean",
the average PWM Score of both strand will be computed. If set to "max",
the highest PWM score between each strand will be selected and finally "sum"
will sum both score together. Default set at "max"
Value
Returns the value assigned to strandRule slot (one of three options :
"mean", "max", "sum") 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
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5
6
7
# Loading data
data(ChIPanalyserData)
#Building data objects
GPP <- parameterOptions( strandRule="max")
#Accesssing Value for strandRule
strandRule(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 strandRule slot in a
parameterOptions object
Usage
1 | strandRule(object)
|
Arguments
object |
|
Details
When computing the PWM Scores and if whichstrand
is set to "+-", strandRule will determine how to handle both strands
( one of three options : "mean", "max", "sum"). If set to "mean",
the average PWM Score of both strand will be computed. If set to "max",
the highest PWM score between each strand will be selected and finally "sum"
will sum both score together. Default set at "max"
Value
Returns the value assigned to strandRule slot (one of three options :
"mean", "max", "sum") 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( strandRule="max")
#Accesssing Value for strandRule
strandRule(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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