parameterOptions-class {ChIPanalyser} | 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.

### See Also

`genomicProfiles`

### Examples

    showClass("parameterOptions")

[Package ChIPanalyser version 1.16.0 Index]