Class "occupancyProfileParameters"

Description

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 from the Class

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 )

Slots

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

Methods

backgroundSignal<-

signature(object = "occupancyProfileParameters", value = "numeric"): Slot Setter Method

backgroundSignal

signature(object = "occupancyProfileParameters"): Slot Accessor Method

boundMolecules<-

signature(object = "occupancyProfileParameters", value = "vector"): Slot Setter Method

boundMolecules

signature(object = "occupancyProfileParameters"): Slot Accessor Method

chipMean<-

signature(object = "occupancyProfileParameters", value = "numeric"): Slot Setter Method

chipMean

signature(object = "occupancyProfileParameters"): Slot Accessor Method

chipSd<-

signature(object = "occupancyProfileParameters", value = "numeric"): Slot Setter Method

chipSd

signature(object = "occupancyProfileParameters"): Slot Accessor Method

chipSmooth<-

signature(object = "occupancyProfileParameters", value = "vector"): Slot Setter Method

chipSmooth

signature(object = "occupancyProfileParameters"):Slot Accessor Method

maxSignal<-

signature(object = "occupancyProfileParameters", value = "numeric"): Slot Setter Method.

maxSignal

signature(object = "occupancyProfileParameters"): Slot Accessor Method

ploidy<-

signature(object = "occupancyProfileParameters", value = "numeric"): Slot Setter Method

ploidy

signature(object = "occupancyProfileParameters"): Slot Accessor Method

removeBackground<-

signature(object = "occupancyProfileParameters", value = "vector"):Slot Setter Method

removeBackground

signature(object = "occupancyProfileParameters"): Slot Setter Method

show

signature(object = "occupancyProfileParameters"): Slot Accessor Method

stepSize<-

signature(object = "occupancyProfileParameters", value = "numeric"): Slot Setter Method

stepSize

signature(object = "occupancyProfileParameters"): Slot Accessor Method

thetaThreshold<-

signature(object = "occupancyProfileParameters", value = "numeric"): Slot Setter Method

thetaThreshold

signature(object = "occupancyProfileParameters"): Slot Accessor Method

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.

See Also

occupancyProfileParameters occupancyProfileParameters-class genomicProfileParameters

Examples

OPP <- occupancyProfileParameters()
# OR
OPP <- occupancyProfileParameters(ploidy=2,
    boundMolecules=5000,backgroundSignal=0)