ChIPanalyser-package {ChIPanalyser} | R Documentation

## ChIPanalyser: Predicting Transcription Factor Binding Sites

### Description

Based on a statistical thermodynamic framework, ChIPanalyser tries to produce ChIP-seq like profile. The model relies on four consideration: TF binding sites can be scored using a Position weight Matrix, DNA accessibility plays a role in Transcription Factor binding, binding profiles are dependant on the number of transcription factors bound to DNA and finally binding energy (another way of describing PWM's) or binding specificity should be modulated (hence the introduction of a binding specificity modulator). The end result of ChIPanalyser is to produce profiles simulating real ChIP-seq profile and provide accuracy measurements of these predicted profiles after being compared to real ChIP-seq data. The ultimate goal is to produce ChIP-seq like profiles predicting ChIP-seq like profile to circumvent the need to produce costly ChIP-seq experiments.

### Details

The DESCRIPTION file:

Package: | ChIPanalyser
Type: | Package
Title: | ChIPanalyser: Predicting Transcription Factor Binding Sites
Authors@R: | c( person(c("Patrick", "CN"), "Martin", role=c("cre", "aut"), email="pm16057@essex.ac.uk"), person(c("Nicolea","Radu"), "Zabet", role="aut"))
Version: | 1.9.1
Date: | 2017-09-01
Author: | Patrick C.N.Martin & Nicolae Radu Zabet
Maintainer: | Patrick C.N. Martin <pm16057@essex.ac.uk>
Citation: | Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
Description: | Based on a statistical thermodynamic framework, ChIPanalyser tries to produce ChIP-seq like profile. The model relies on four consideration: TF binding sites can be scored using a Position weight Matrix, DNA accessibility plays a role in Transcription Factor binding, binding profiles are dependant on the number of transcription factors bound to DNA and finally binding energy (another way of describing PWM's) or binding specificity should be modulated (hence the introduction of a binding specificity modulator). The end result of ChIPanalyser is to produce profiles simulating real ChIP-seq profile and provide accuracy measurements of these predicted profiles after being compared to real ChIP-seq data. The ultimate goal is to produce ChIP-seq like profiles predicting ChIP-seq like profile to circumvent the need to produce costly ChIP-seq experiments.
License: | GPL-3
Collate: | 2AllS4Class_ProfileParameters.R 3AllGenerics.R 4AllMethods.R AllInitialize.R AllShowMethods.R computeChIPProfile.R computeOccupancy.R computeOptimal.R computePWMScore.R computeGenomeWide.R parallelInternalFunctionsDev.R GenomicProfileGenericFunctions.R plotOccupancyDev.R plotOptimalHeatMapDev.R DataPreprocessingDev.R DataPreprocessingGenericFunctionsDev.R profileAccuracyEstimateDev.R
Depends: | R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel
Imports: | methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb
Suggests: | BSgenome.Dmelanogaster.UCSC.dm3,knitr, RUnit, BiocGenerics
Encoding: | UTF-8
LazyData: | true
biocViews: | Software, BiologicalQuestion, WorkflowStep, Transcription, Sequencing, ChipOnChip, Coverage, Alignment, ChIPSeq, SequenceMatching, DataImport ,PeakDetection
VignetteBuilder: | knitr
git_url: | https://git.bioconductor.org/packages/ChIPanalyser
git_branch: | master
git_last_commit: | 432ad12
git_last_commit_date: | 2019-11-12
Date/Publication: | 2019-11-12

Index of help topics:

    BPFrequency             Accessor method for 'BPFrequency' slot in a
                            'genomicProfiles' object.
    BPFrequency-methods     ~~ Methods for Function 'BPFrequency' ~~
    BPFrequency<-           Setter method for 'BPFrequency' slot in a
                            'genomicProfiles' object.
    BPFrequency<--methods   ~~ Methods for Function 'BPFrequency<-' ~~
    ChIPScore-class         Class '"ChIPScore"'
    ChIPanalyser            ChIPanalyser: Predicting Transcription Factor
                            Binding Sites
    ChIPanalyserData        ChIPanalyserData
    DNASequenceLength       Accessor method for 'DNASequenceLength' slot in
                            a 'genomicProfiles'
    DNASequenceLength-methods
                            ~~ Methods for Function 'DNASequenceLength' ~~
    GRList-class            Class '"GRList"'
    PFMFormat               Accesor method for the 'PFMFormat' slot in a
                            'genomicProfiles' object
    PFMFormat-methods       ~~ Methods for Function 'PFMFormat' ~~
    PFMFormat<-             Setter method for the 'PFMFormat' slot in a
                            'genomicProfiles' object
    PFMFormat<--methods     ~~ Methods for Function 'PFMFormat<-' ~~
    PWMThreshold            Accessor method for the 'PWMThreshold' slot in
                            a 'parameterOptions' object
    PWMThreshold-methods    ~~ Methods for Function 'PWMThreshold' ~~
    PWMThreshold<-          Setter Method for the 'PWMThreshold' slot in a
                            'parameterOptions' object
    PWMThreshold<--methods
                            ~~ Methods for Function 'PWMThreshold<-' ~~
    PWMpseudocount          Accessor Method for a 'PWMpseudocount' slot in
                            a 'parameterOptions'
    PWMpseudocount-methods
                            ~~ Methods for Function 'PWMpseudocount' ~~
    PWMpseudocount<-        Setter Method for the 'pseudocount' slot in a
                            'parameterOptions' object
    PWMpseudocount<--methods
                            ~~ Methods for Function 'PWMpseudocount<-' ~~
    PositionFrequencyMatrix
                            Accessor method for the 'PFM' slot in a
                            'genomicProfiles' object
    PositionFrequencyMatrix-methods
                            ~~ Methods for Function
                            'PositionFrequencyMatrix' ~~
    PositionFrequencyMatrix<-
                            Setter method for the 'PFM' slot in a
                            'genomicProfiles' object
    PositionFrequencyMatrix<--methods
                            ~~ Methods for Function
                            'PositionFrequencyMatrix<-' ~~
    PositionWeightMatrix    Accessor Method for the 'PWM' slot in a
                            'genomicProfiles' object
    PositionWeightMatrix-methods
                            ~~ Methods for Function 'PositionWeightMatrix'
                            ~~
    PositionWeightMatrix<-
                            Setter Method for the 'PositionWeightMatrix'
                            slot in a 'genomicProfiles' object
    PositionWeightMatrix<--methods
                            ~~ Methods for Function
                            'PositionWeightMatrix<-' ~~
    averageExpPWMScore      Accessor for 'averageExpPWMScore' slot in a
                            'genomicProfiles' object.
    averageExpPWMScore-methods
                            ~~ Methods for Function 'averageExpPWMScore' ~~
    backgroundSignal        Accessor method for the 'backgroundSignal' slot
                            in a 'parameterOptions' object.
    backgroundSignal-methods
                            ~~ Methods for Function 'backgroundSignal' ~~
    backgroundSignal<-      Setter method for 'backgroundSignal' slot in a
                            'parameterOptions'
    backgroundSignal<--methods
                            ~~ Methods for Function 'backgroundSignal<-' ~~
    boundMolecules          Accessor methods for 'boundMolecules' slot in
                            'parameterOptions' object.
    boundMolecules-methods
                            ~~ Methods for Function 'boundMolecules' ~~
    boundMolecules<-        Setter method for the 'boundMolecules' slot in
                            a 'parameterOptions' object.
    boundMolecules<--methods
                            ~~ Methods for Function 'boundMolecules<-' ~~
    chipMean                Accessor method for 'chipMean' slot in a
                            'parameterOptions' object.
    chipMean-methods        ~~ Methods for Function 'chipMean' ~~
    chipMean<-              Access methods for 'chipMean' slot in
                            'parameterOptions' object.
    chipMean<--methods      ~~ Methods for Function 'chipMean<-' ~~
    chipSd                  Accessor method for 'chipSd' slot in a
                            'parameterOptions' object.
    chipSd-methods          ~~ Methods for Function 'chipSd' ~~
    chipSd<-                Setter methods for 'chipSd' slot in a
                            'parameterOptions' object.
    chipSd<--methods        ~~ Methods for Function 'chipSd<-' ~~
    chipSmooth              Accessor methods for 'chipSmooth' slot in a
                            'parameterOptions' object.
    chipSmooth-methods      ~~ Methods for Function 'chipSmooth' ~~
    chipSmooth<-            Setter method for 'chipSmooth' slot in
                            'parameterOptions' object.
    chipSmooth<--methods    ~~ Methods for Function 'chipSmooth<-' ~~
    computeChIPProfile      Computing ChIP-seq like profiles from Occupancy
                            data.
    computeGenomeWideScores
                            Computing Genome Wide scores
    computeOccupancy        Compute Occupancy values from PWM Scores based
                            on model.
    computeOptimal          compute Optimal Parameters
    computePWMScore         Compute PWM Scores of sites above threshold.
    drop                    Accessor Method for the 'drop' slot in a
                            'genomicProfiles' object.
    drop-methods            ~~ Methods for Function 'drop' ~~
    genomicProfiles         Genomic Profile object
    genomicProfiles-class   Class '"genomicProfiles"'
    genomicProfilesInternal-class
                            Class '"genomicProfilesInternal"'
    initialize-methods      ~~ Methods for Function 'initialize' ~~
    lambdaPWM               Accessor Method for the 'lambdaPWM' slot in a
                            'parameterOptions' object
    lambdaPWM-methods       ~~ Methods for Function 'lambdaPWM' ~~
    lambdaPWM<-             Setter Method for the 'lambdaPWM' slot in a
                            'parameterOptions' object
    lambdaPWM<--methods     ~~ Methods for Function 'lambdaPWM<-' ~~
    loci                    Accessor Method for the 'loci' slot in a
                            'ChIPScore' object
    loci-class              Class '"loci"'
    loci-methods            ~~ Methods for Function 'loci' ~~
    lociWidth               Accessor Method for the 'lociWidth' slot in a
                            'parameterOptions' object
    lociWidth-methods       ~~ Methods for Function 'lociWidth' ~~
    lociWidth<-             Setter Method for the 'lociWidth' slot in a
                            'parameterOptions' object
    lociWidth<--methods     ~~ Methods for Function 'lociWidth<-' ~~
    maxPWMScore             Accessor function for 'maxPWMScore' slot in a
                            'genomicProfiles' object.
    maxPWMScore-methods     ~~ Methods for Function 'maxPWMScore' ~~
    maxSignal               Accessor method for the 'maxSignal' slot in a
                            'parameterOptions' object.
    maxSignal-methods       ~~ Methods for Function 'maxSignal' ~~
    maxSignal<-             Setter method for 'maxSignal' slot in a
                            'parameterOptions' object.
    maxSignal<--methods     ~~ Methods for Function 'maxSignal<-' ~~
    minPWMScore             Accessor method the 'minPWMScore' slot in a
                            'genomicProfiles' object
    minPWMScore-methods     ~~ Methods for Function 'minPWMScore' ~~
    naturalLog              Accessor method the 'naturalLog' slot in a
                            'parameterOptions' object.
    naturalLog-methods      ~~ Methods for Function 'naturalLog' ~~
    naturalLog<-            Setter method for the 'naturalLog' slot in a
                            'parameterOptions' object.
    naturalLog<--methods    ~~ Methods for Function 'naturalLog<-' ~~
    noOfSites               Accessor Method for the 'noOfSites' slot in a
                            'parameterOptions' object
    noOfSites-methods       ~~ Methods for Function 'noOfSites' ~~
    noOfSites<-             Setter Method for the 'noOfSites' slot in a
                            'parameterOptions' object.
    noOfSites<--methods     ~~ Methods for Function 'noOfSites<-' ~~
    noiseFilter             Accessor Method for the 'noiseFilter' slot in a
                            'parameterOptions' object
    noiseFilter-methods     ~~ Methods for Function 'noiseFilter' ~~
    noiseFilter<-           Setter Method for the 'noiseFilter' slot in a
                            'parameterOptions' object
    noiseFilter<--methods   ~~ Methods for Function 'noiseFilter<-' ~~
    nos-class               Class '"nos"'
    parameterOptions        parameter Options object
    parameterOptions-class
                            Class '"parameterOptions"'
    ploidy                  Accessor method for the 'ploidy' slot in a
                            'parameterOptions' object
    ploidy-methods          ~~ Methods for Function 'ploidy' ~~
    ploidy<-                Setter Method for the 'ploidy' slot in an
                            'parameterOptions' object
    ploidy<--methods        ~~ Methods for Function 'ploidy<-' ~~
    plotOccupancyProfile    Plot Occupancy Profiles
    plotOptimalHeatMaps     Heat Map of optimal Parameters
    processingChIP          Pre-processing ChIP-seq data
    profileAccuracyEstimate
                            Estimating Accuracy of predicted Profiles
    profiles                ~~ Methods for Function 'profiles' ~~
    removeBackground        Accessor Method for the 'removeBackground' slot
                            in a 'parameterOptions' object
    removeBackground-methods
                            ~~ Methods for Function 'removeBackground' ~~
    removeBackground<-      Setter Method for the 'removeBackground' slot
                            in a 'parameterOptions' object
    removeBackground<--methods
                            ~~ Methods for Function 'removeBackground<-' ~~
    scores                  Accessor Method for the 'scores' slot in a
                            'ChIPScore' object
    scores-methods          ~~ Methods for Function 'scores' ~~
    searchSites             Searching function for Sites above threshold
                            and predicted ChIP-seq Profiles
    show-methods            ~~ Methods for Function 'show' ~~
    stepSize                Accessor method of the 'stepSize' slot in
                            'parameterOptions' object
    stepSize-methods        ~~ Methods for Function 'stepSize' ~~
    stepSize<-              Setter Method for the 'stepSize' slot in a
                            'parameterOptions'
    stepSize<--methods      ~~ Methods for Function 'stepSize<-' ~~
    strandRule              Accessor Method for the 'strandRule' slot in a
                            'parameterOptions' object
    strandRule-methods      ~~ Methods for Function 'strandRule' ~~
    strandRule<-            Setter method for the 'strandRule' slot in a
                            'parameterOptions' object.
    strandRule<--methods    ~~ Methods for Function 'strandRule<-' ~~
    whichstrand             Accessor method for the 'whichstrand' slot in a
                            'parameterOptions' object
    whichstrand-methods     ~~ Methods for Function 'whichstrand' ~~
    whichstrand<-           Setter method for the 'whichstrand' slot in a
                            'parameterOptions' object
    whichstrand<--methods   ~~ Methods for Function 'whichstrand<-' ~~

### Author(s)

Patrick C.N. Martin <pm16057@essex.ac.uk>

And

Nicolae Radu Zabet <nzabet@essex.ac.uk>

Maintainer: Patrick C.N. Martin <pm16057@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.

### 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)){
        if (!requireNamespace("BiocManager", quietly=TRUE))
            install.packages("BiocManager")
        BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")
    }
    library(BSgenome.Dmelanogaster.UCSC.dm3)
    DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)
    #Building data objects
    GPP <- genomicProfiles(PFM=PFM,PFMFormat="raw",BPFrequency=DNASequenceSet)

    eveLocusChip<-processingChIP(eveLocusChip,eveLocus)
    # Computing Genome Wide
    GenomeWide <- computeGenomeWideScores(DNASequenceSet = DNASequenceSet,
        genomicsProfiles = GPP)

    #Compute PWM Scores
    PWMScores <- computePWMScore(genomicsProfiles = GenomeWide,
        DNASequenceSet = DNASequenceSet,
        loci = eveLocus, chromatinState = Access)
    #Compute Occupnacy
    Occupancy <- computeOccupancy(genomicsProfiles = PWMScores,
        parameterOptions = OPP)

    #Compute ChIP profiles
    chipProfile <- computeChIPProfile(genomicProfiles = Occupancy,
         loci = eveLocus,
        parameterOptions = OPP)
    #Estimating accuracy estimate
    AccuracyEstimate <- profileAccuracyEstimate(genomicProfiles = chipProfile,
         ChIPScore = eveLocusChip,
         parameterOptions = OPP)

[Package ChIPanalyser version 1.9.1 Index]