parameterOptions {ChIPanalyser} | R Documentation

## parameter Options object

### Description

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

### Usage

    parameterOptions(ploidy = 2, boundMolecules = 1000, backgroundSignal = 0, maxSignal = 1, lociWidth = 20000, chipMean = 200, chipSd = 200, chipSmooth = 250, stepSize = 10, removeBackground = 0, noiseFilter = "zero", naturalLog = TRUE, noOfSites = "all", PWMThreshold = 0.7, strandRule = "max", whichstrand = "+-", PWMpseudocount = 1, lambdaPWM = 1)

### Arguments

`ploidy` | `ploidy`: A numeric Value descibing the ploidy of the organism. Default: 2
`boundMolecules` | `boundMolecules`: A vector (or single value) containing the number of bound Molecules (bound Transcription Factors): Default: 1000
`backgroundSignal` | `backgroundSignal`: A numeric value descibing the ChIP-seq background Signal (average signal from real ChIP seq data). Default: 0
`maxSignal` | `maxSignal`: A numeric value describing the highest ChIP-seq signal (from real ChIP-seq data). Default: 1
`lociWidth` | `lociWidth`: A numeric value describing the width of the bins used to split ChIP profiles parsed to `processingChIP`. Default = 20000
`chipMean` | `chipMean`: A numeric value describing the mean width of a ChIP- seq peak: Default:200
`chipSd` | `chipSd`: A numeric value describing the standard deviation of ChIP-seq peaks. Default: 200
`chipSmooth` | `chipSmooth`: A numeric value describing the width of the window used to smooth Occupancy profiles into ChIP profiles. Default:250
`stepSize` | `stepSize`: A numeric value describing the step Size (in base pairs) between each ChIP-seq score. Default:10 (Scored every 10 base pairs)
`removeBackground` | `removeBackground`: A numeric value describing the value at which score should be removed. Defualt:0 (If negative scores then remove)
`noiseFilter` | `noiseFilter`: A character string of one of the following: Zero, Mean, Median, or Sigmoid. Noise filter that will be applied to the ChIP Score during the `processingChIP` step.
`naturalLog` | `naturalLog`: A logical value describing if natural Log will be used to compute the PWM (if FALSE then log2 will be used). Default: TRUE
`noOfSites` | `noOfSites`: 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)
`PWMThreshold` | `PWMThreshold`: Threshold at which PWM Score should be selected (only sites above threshold will be selected - between 0 and 1)
`strandRule` | `strandRule`: ‘mean’, ‘max’ or ‘sum’ will dertermine how strand should be handle for computing PWM Scores. Default : ‘max’
`whichstrand` | `whichstrand`: ‘+’,‘-’ or ‘+-’ on which strand should PWM Score be computed. Default: ‘+-’
`PWMpseudocount` | `PWMpseudocount`: A numeric value describing a PWMpseudocount for PWM computation. Default:1
`lambdaPWM` | A vector (or single value) contaning values for the ScalingFactorPWM (Also known as lambda).Default:1

### Details

ChIPanalyser requires a lot of parameters. `parameterOptions` was created with the intent of storing and parsing these numerous arguments to the different functions. All parameters in this object are optional although strongly recommend. Some parameters are extracted and updated from function along the pipeline e.g. maxSignal and backgroundSignal are extracted during the `processingChIP` step. These paramters will be automatically parsed. If you do not which to use them ( or any other parameter) simply parse a new parameterOptions object with your desired paramters.

### Value

Returns a `parameterOptions` with updated values.

### Author(s)

Patrick 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

    #
    parameterOptions(ploidy = 2, boundMolecules = 1000, backgroundSignal = 0,
        maxSignal = 1, lociWidth = 20000, chipMean = 200, chipSd = 200,
        chipSmooth = 250, stepSize = 10, removeBackground = 0, noiseFilter = "zero",
        naturalLog = TRUE, noOfSites = "all", PWMThreshold = 0.7,
        strandRule = "max", whichstrand = "+-", PWMpseudocount = 1,
        lambdaPWM = 1)

[Package ChIPanalyser version 1.8.0 Index]