genomicProfileParameters-class {ChIPanalyser} | R Documentation

## Class `"genomicProfileParameters"`

### Description

`genomicProfileParameters` is a data/parameter storing object. The main purpose of this object is to store parameters neccessary for further computation but also store results. This makes parsing data and parameters easier between the different of functions available in `ChIPanalyser`.

### Objects from the Class

Objects can be created by calls of the form `genomicProfileParameters(PWM, PFM,PFMFormat, ScalingFactorPWM, PWMpseudocount, BPFrequency, naturalLog, noOfSites, minPWMScore, maxPWMScore, PWMThreshold, AllSitesAboveThreshold, DNASequenceLength , averageExpPWMScore , strandRule , whichstrand, NoAccess)`. `PWM` and `PFM` slots are the only slots that are absolutely required (At least one of the two). All other slots have a provided default value. We strongly advise you to tailor these parameters to increase goodness of fit between the predcited model and real ChIP-seq data.

### 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

`ScalingFactorPWM`:

  Object of class `"vector"`: A vector (or single value) contaning values for the ScalingFactorPWM (Also known as lambda).Default:1

`PWMpseudocount`:

  Object of class `"numeric"`: A numeric value describing a PWMpseudocount for PWM computation. Default:1

`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)

`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 `"vector"`: 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)

`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)

`PWMThreshold`:

  Object of class `"numeric"`: Threshold at which PWM Score should be selected (only sites above threshold will be selected - between 0 and 1)

`AllSitesAboveThreshold`:

  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

`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: "+-"

`NoAccess`:

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

`ZeroBackground`:

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

### Extends

Class `occupancyProfileParameters`, directly.

### Methods

AllSitesAboveThreshold

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

averageExpPWMScore

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

BPFrequency<-

  `signature(object = "genomicProfileParameters", value = "vector")`:Slot Setter Method

BPFrequency<-

  `signature(object = "genomicProfileParameters", value = "DNAStringSet")`:Slot Setter Method

BPFrequency

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

DNASequenceLength<-

  `signature(object = "genomicProfileParameters", value = "vector")`: Slot Setter Method

DNASequenceLength

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

maxPWMScore

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

minPWMScore

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

naturalLog<-

  `signature(object = "genomicProfileParameters", value = "logical")`: Slot Setter Method

naturalLog

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

NoAccess

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

noOfSites<-

  `signature(object = "genomicProfileParameters", value = "vector")`: Slot Setter Method

noOfSites

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

PositionFrequencyMatrix<-

  `signature(object = "genomicProfileParameters", value = "matrix")`: Slot Setter Method

PositionFrequencyMatrix<-

  `signature(object = "genomicProfileParameters", value = "character")`: Slot Setter Method

PositionFrequencyMatrix

  `signature(object = "genomicProfileParam"`: Slot Accessor Method

PFMFormat<-

  `signature(object = "genomicProfileParameters", value = "character")`: Slot Setter Method

PFMFormat

  `signature(object = "genomicProfileParam"`: Slot Accessor Method

PositionWeightMatrix<-

  `signature(object = "genomicProfileParameters", value = "matrix")`:Slot Setter Method

PositionWeightMatrix

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

PWMpseudocount<-

  `signature(object = "genomicProfileParameters", value = "numeric")`: Slot Setter Method

PWMpseudocount

  `signature(object = "genomicProfileParameters")`:Slot Accessor Method

PWMThreshold<-

  `signature(object = "genomicProfileParameters", value = "numeric")`: Slot Setter Method

PWMThreshold

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

ScalingFactorPWM<-

  `signature(object = "genomicProfileParameters", value = "vector")`: Slot Setter Method

ScalingFactorPWM

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

strandRule<-

  `signature(object = "genomicProfileParameters", value = "character")`: Slot Setter Method

strandRule

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

whichstrand<-

  `signature(object = "genomicProfileParameters", value = "character")`: Slot Setter Method

whichstrand

  `signature(object = "genomicProfileParameters")`: Slot Accessor Method

### 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

`genomicProfileParameters` `occupancyProfileParameters-class` `occupancyProfileParameters`

### Examples

    #Data extraction
    data(ChIPanalyserData)
    # path to Position Frequency Matrix
    PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
    #As an example of genome, this example will run on the Drosophila genome

    if(!require("BSgenome.Dmelanogaster.UCSC.dm3", character.only = TRUE)){
        source("https://bioconductor.org/biocLite.R")
        biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
    }
    library(BSgenome.Dmelanogaster.UCSC.dm3)
    DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)

    # Building genomicProfileParameters object
    GPP <- genomicProfileParameters(PFM=PFM, ScalingFactorPWM=c(1,1.5,2),
        BPFrequency=DNASequenceSet)

[Package ChIPanalyser version 1.2.0 Index]