parameterOptions-class: Class '"parameterOptions"'
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

parameterOptions-class

R Documentation

Class `"parameterOptions"`

Description

parameterOptions is an object used to store and parse the various parameters needed throughout this analysis pipeline.

Objects from the Class

Objects can be created by calls of the form parameterOptions(ploidy, boundMolecules, backgroundSignal, maxSignal, lociWidth, chipMean, chipSd, chipSmooth, stepSize, noiseFilter, removeBackground, lambdaPWM, PWMpseudocount, naturalLog, noOfSites, PWMThreshold, strandRule, whichstrand).

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
lociWidth:: Object of class "numeric": A numeric value describing bin size when splitting ChIP seq scores). Default: 20 000
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)
noiseFilter:: Object of class "character" Describes noiseFilter method applied to ChIP scores
PWMThreshold:: Object of class "numeric": Threshold at which PWM Score should be selected (only sites above threshold will be selected - between 0 and 1)
strandRule:: Object of class "character": "mean", "max" or "sum" will dertermine how strand should be handle for computing PWM Scores. Default : "max"
whichstrand:: Object of class "character": "+","-" or "+-" on which strand should PWM Score be computed. Default: "+-"
lambdaPWM:: Object of class "vector" A vector (or single value) contaning values for lambdaPWM Default:1
naturalLog:: Object of class "logical": A logical value describing if natural Log will be used to compute the PWM (if FALSE then log2 will be used). Default: TRUE
noOfSites:: Object of class "nos" A Positive integer descibing number of sites (in base pair) should be used from the PFM to compute PWM. Default =0 (Full width of binding site will be used when set to 0)
PWMpseudocount:: Object of class "numeric": A numeric value describing a PWMpseudocount for PWM computation. Default:1
paramTag:: Object of class "character" ~Internal~

Methods

.paramTag: signature(object = "parameterOptions"): ...
.paramTag<-: signature(object = "parameterOptions", value = "character"): ...
.ZeroBackground: signature(object = "parameterOptions"): ...
.ZeroBackground<-: signature(object = "parameterOptions", value = "vector"): ...
backgroundSignal: signature(object = "parameterOptions"): ...
backgroundSignal<-: signature(object = "parameterOptions", value = "numeric"): ...
boundMolecules: signature(object = "parameterOptions"): ...
boundMolecules<-: signature(object = "parameterOptions", value = "vector"): ...
chipMean: signature(object = "parameterOptions"): ...
chipMean<-: signature(object = "parameterOptions", value = "numeric"): ...
chipSd: signature(object = "parameterOptions"): ...
chipSd<-: signature(object = "parameterOptions", value = "numeric"): ...
chipSmooth: signature(object = "parameterOptions"): ...
chipSmooth<-: signature(object = "parameterOptions", value = "vector"): ...
initialize: signature(.Object = "parameterOptions"): ...
lambdaPWM: signature(object = "parameterOptions"): ...
lambdaPWM<-: signature(object = "parameterOptions", value = "vector"): ...
lociWidth: signature(object = "parameterOptions"): ...
lociWidth<-: signature(object = "parameterOptions", value = "numeric"): ...
maxSignal: signature(object = "parameterOptions"): ...
maxSignal<-: signature(object = "parameterOptions", value = "numeric"): ...
naturalLog: signature(object = "parameterOptions"): ...
naturalLog<-: signature(object = "parameterOptions", value = "logical"): ...
noiseFilter: signature(object = "parameterOptions"): ...
noiseFilter<-: signature(object = "parameterOptions", value = "character"): ...
noOfSites: signature(object = "parameterOptions"): ...
noOfSites<-: signature(object = "parameterOptions", value = "character"): ...
noOfSites<-: signature(object = "parameterOptions", value = "numeric"): ...
ploidy: signature(object = "parameterOptions"): ...
ploidy<-: signature(object = "parameterOptions", value = "numeric"): ...
PWMpseudocount: signature(object = "parameterOptions"): ...
PWMpseudocount<-: signature(object = "parameterOptions", value = "numeric"): ...
PWMThreshold: signature(object = "parameterOptions"): ...
PWMThreshold<-: signature(object = "parameterOptions", value = "numeric"): ...
removeBackground: signature(object = "parameterOptions"): ...
removeBackground<-: signature(object = "parameterOptions", value = "vector"): ...
show: signature(object = "parameterOptions"): ...
stepSize: signature(object = "parameterOptions"): ...
stepSize<-: signature(object = "parameterOptions", value = "numeric"): ...
strandRule: signature(object = "parameterOptions"): ...
strandRule<-: signature(object = "parameterOptions", value = "character"): ...
whichstrand: signature(object = "parameterOptions"): ...
whichstrand<-: signature(object = "parameterOptions", value = "character"): ...

Author(s)

Partick C. N. Martin <p.martin@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. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.