parameterOptions: parameter Options object

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

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 <[e-mail]>

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)

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.