backgroundSignal: Accessor method for the 'backgroundSignal' slot in a...
In patrickCNMartin/ChIPanalyserDev: ChIPanalyser: Predicting Transcription Factor Binding Sites
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
Extract or access the backgroundSignal slot in a
parameterOptions object.
Usage
1
backgroundSignal(object)
Arguments
object
object is an parameterOptions
Details
Default Value: 0
When computing computeOccupancy, a ChIP-seq background
signal is used to scale Occupancy by considering both a
backgroundSignal and a maxSignal.
The backgroundSignal
is also used to nomalise occupancies against maxOccupancy.
The backgroundSignal usually comes from
experimental data and is provided by user. As a general rule,
if ChIP-seq data is available and will be used in
computeChIPProfile
, profileAccuracyEstimate or plotOccupancyProfile,
it is advised to use the backgroundSignal from this data.
We strongly encourage to set values when building a
parameterOptions object.
Value
Returns a backgroundSignal of 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
# Building occupancyProfileParameters object
OPP <- parameterOptions()
#Viewing single value in object
backgroundSignal(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
Extract or access the backgroundSignal slot in a
parameterOptions object.
Usage
1 | backgroundSignal(object)
|
Arguments
object |
|
Details
Default Value: 0
When computing computeOccupancy, a ChIP-seq background
signal is used to scale Occupancy by considering both a
backgroundSignal and a maxSignal.
The backgroundSignal
is also used to nomalise occupancies against maxOccupancy.
The backgroundSignal usually comes from
experimental data and is provided by user. As a general rule,
if ChIP-seq data is available and will be used in
computeChIPProfile
, profileAccuracyEstimate or plotOccupancyProfile,
it is advised to use the backgroundSignal from this data.
We strongly encourage to set values when building a
parameterOptions object.
Value
Returns a backgroundSignal of 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 | # Building occupancyProfileParameters object
OPP <- parameterOptions()
#Viewing single value in object
backgroundSignal(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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