occupancyProfileParameters-class {ChIPanalyser} | R Documentation |
"occupancyProfileParameters"
occupancyProfileParameters
is a parameter storage object.
Similarly to genomicProfileParameters
,
this object serves the purpose of handling the set of parameters needed
when using certain functions.
Objects can be created by calls of the form
occupancyProfileParameters(ploidy = 2 , boundMolecules = 1000 ,
backgroundSignal = 0 , maxSignal = 1 , chipMean = 150 , chipSd = 150 ,
chipSmooth = 250 , stepSize = 10 , removeBackground = 0 ,
thetaThreshold = 0.1 )
ploidy
:Object of class "numeric"
:
A numeric Value descibing the ploidy of the organism. Default: 2
boundMolecules
:Object of class "vector"
:
A vector (or single value) containing the number of bound Molecules
(bound Transcription Factors): Default: 1000
backgroundSignal
:Object of class "numeric"
:
A numeric value descibing the ChIP-seq background Signal
(average signal from real ChIP seq data). Default: 0
maxSignal
:Object of class "numeric"
:
A numeric value describing the highest ChIP-seq signal
(from real ChIP-seq data). Default: 1
chipMean
:Object of class "numeric"
:
A numeric value describing the mean width of a ChIP- seq peak.
Default:150
chipSd
:Object of class "numeric"
:
A numeric value describing the standard deviation of ChIP-seq peaks.
Default: 150
chipSmooth
:Object of class "vector"
:
A numeric value describing the width of the window used to smooth
Occupancy profiles into ChIP profiles. Default:250
stepSize
:Object of class "numeric"
:
A numeric value describing the step Size (in base pairs) between
each ChIP-seq score. Default:10 (Scored every 10 base pairs)
removeBackground
:Object of class "numeric"
:
A numeric value describing the value at which score should be removed.
Defualt:0 (If negative scores then remove)
thetaThreshold
:Object of class "numeric"
:
A numeric value describing a threshold at which low ratios of correlation
over Mean Squared Error (
for accuracy estimation) should be removed. Default: 0.1
signature(object =
"occupancyProfileParameters", value = "numeric")
: Slot Setter Method
signature(object =
"occupancyProfileParameters")
: Slot Accessor Method
signature(object =
"occupancyProfileParameters", value = "vector")
: Slot Setter Method
signature(object =
"occupancyProfileParameters")
: Slot Accessor Method
signature(object =
"occupancyProfileParameters", value = "numeric")
: Slot Setter Method
signature(object =
"occupancyProfileParameters")
: Slot Accessor Method
signature(object =
"occupancyProfileParameters", value = "numeric")
: Slot Setter Method
signature(object =
"occupancyProfileParameters")
: Slot Accessor Method
signature(object =
"occupancyProfileParameters", value = "vector")
: Slot Setter Method
signature(object =
"occupancyProfileParameters")
:Slot Accessor Method
signature(object =
"occupancyProfileParameters", value = "numeric")
: Slot Setter Method.
signature(object =
"occupancyProfileParameters")
: Slot Accessor Method
signature(object =
"occupancyProfileParameters", value = "numeric")
: Slot Setter Method
signature(object =
"occupancyProfileParameters")
: Slot Accessor Method
signature(object =
"occupancyProfileParameters", value = "vector")
:Slot Setter Method
signature(object =
"occupancyProfileParameters")
: Slot Setter Method
signature(object =
"occupancyProfileParameters")
: Slot Accessor Method
signature(object =
"occupancyProfileParameters", value = "numeric")
: Slot Setter Method
signature(object =
"occupancyProfileParameters")
: Slot Accessor Method
signature(object =
"occupancyProfileParameters", value = "numeric")
: Slot Setter Method
signature(object =
"occupancyProfileParameters")
: Slot Accessor Method
Patrick C. N. Martin <pm16057@essex.ac.uk>
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
occupancyProfileParameters
occupancyProfileParameters-class
genomicProfileParameters
OPP <- occupancyProfileParameters() # OR OPP <- occupancyProfileParameters(ploidy=2, boundMolecules=5000,backgroundSignal=0)