chipMean: Accessor method for 'chipMean' 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 for chipMean slot in a
parameterOptions object.
Usage
1
chipMean(object)
Arguments
object
object is a parameterOptions
Details
Default vlaue : 150
When computing ChIP-seq like profiles (computeChIPProfile,
the occupancy values given by computeOccupancy are transformed
into ChIP-seq like profiles.
The average size of a ChIP-seq peak was described by Kaplan
(Kaplan et al. , 2011). It is advised to use the average
width of ChIP peaks from actual ChIP-seq data.
We strongly encourage to set values when building a
parameterOptions object.
Value
Returns chipMean slot from 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.
Kaplan T.,Li X.-Y.,Sabo P.J.,Thomas S.,Stamatoyannopoulos J.A., Biggin M.D.,
EisenM.B.
Quantitative models of the mechanisms that control genome-wide patterns of
transcription factor binding during early Drosophila development,
PLoS Genet.,2011, vol. 7 pg. e1001290
Examples
1
2
3
4
# Building parameterOptions object
OPP <- parameterOptions()
#Accessing chipMean slot in OPP
chipMean(OPP)
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 chipMean slot in a
parameterOptions object.
Usage
1 | chipMean(object)
|
Arguments
object |
|
Details
Default vlaue : 150
When computing ChIP-seq like profiles (computeChIPProfile,
the occupancy values given by computeOccupancy are transformed
into ChIP-seq like profiles.
The average size of a ChIP-seq peak was described by Kaplan
(Kaplan et al. , 2011). It is advised to use the average
width of ChIP peaks from actual ChIP-seq data.
We strongly encourage to set values when building a
parameterOptions object.
Value
Returns chipMean slot from 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.
Kaplan T.,Li X.-Y.,Sabo P.J.,Thomas S.,Stamatoyannopoulos J.A., Biggin M.D., EisenM.B. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development, PLoS Genet.,2011, vol. 7 pg. e1001290
Examples
1 2 3 4 | # Building parameterOptions object
OPP <- parameterOptions()
#Accessing chipMean slot in OPP
chipMean(OPP)
|
R Package Documentation
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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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