genomicProfiles-class {ChIPanalyser} | R Documentation

## Class `"genomicProfiles"`

### Description

`genomicProfiles` is an S4 object serving two purposes: (i) storing internal computed data and (ii) storing paramter options. This object is parsed through the different steps of the pipeline to facilitate that parsing and changing of paramters.

### Objects from the Class

Objects can be created by calls of the form `genomicProfiles(ploidy, boundMolecules, backgroundSignal, maxSignal, lociWidth, chipMean, chipSd, chipSmooth, stepSize, noiseFilter, removeBackground, lambdaPWM, PWMpseudocount, naturalLog, noOfSites, PWMThreshold, strandRule, whichstrand, PFM, PWM, PFMFormat, BPFrequency, minPWMScore, maxPWMScore, profiles, DNASequenceLength, averageExpPWMScore)`.

### Slots

`PWM`:

  Object of class `"matrix"`: A Position Weight Matrix (either supplied or internally computed if PFM is provided)

`PFM`:

  Object of class `"matrix"`: A Position Frequency Matrix (may also be a path to file containing PFM)

`PFMFormat`:

  Object of class `"character"`: A character string of one of the following: raw, transfac,JASPAR or sequences

`BPFrequency`:

  Object of class `"vector"`: Base Pair Frequency in the genome (if a DNA sequence is provided (as a `DNAStringSet` or `BSgenome`), will be automatically computed internally). Default:c(0.25,0.25,0.25,0.25)

`minPWMScore`:

  Object of class `"vector"`: Lowest PWM score accros the genome (computed and updated internally)

`maxPWMScore`:

  Object of class `"vector"`: Highest PWM score across the genome (computed and updated internally)

`profiles`:

  Object of class `"GRList"`: Containins GRanges with sites above threshold and associated metrics (PWMscore and Occupancy) - Computed Internally

`DNASequenceLength`:

  Object of class `"vector"`: Length of the Genome (or accesible genome) - computed internally

`averageExpPWMScore`:

  Object of class `"vector"`: Average exponential PWM score across the genome (or accesible genome) - computed internally

`ZeroBackground`:

  Object of class `"vector"`: Internal background value (computed internally)

`drop`:

  Object of class `"vector"`: Stores Loci that do contain accesible DNA if it were to be the case (computed and updated internally)

`tags`:

  Object of class `"character"` ~Internal Tags~

`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"` ~~

`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 the noiseFilter method that will be applied to ChIP data (Zero, mean, median, sigmoid)~

`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~

### Extends

Class `"genomicProfilesInternal"`, directly. Class `"parameterOptions"`, directly.

### Methods

initialize

  `signature(.Object = "genomicProfiles")`: ...

show

  `signature(object = "genomicProfiles")`: ...

### 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` `parameterOptions`

### Examples

    showClass("genomicProfiles")

[Package ChIPanalyser version 1.16.0 Index]