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: | 1.2.0
Date: | 2017-09-01
Author: | Patrick C.N.Martin & Nicolae Radu Zabet
Maintainer: | Patrick C.N. Martin <pm16057@essex.ac.uk>
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 genomeWidePWM.R parallelInternalFunctions.R GenomicProfileGenericFunctions.R plotOccupancyDev.R plotOptimalHeatMaps.R DataPreprocessing.R DataPreprocessingGenericFunctions.R profileAccuracyEstimate.R
Depends: | R (>= 3.4.1),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel
Imports: | methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer
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

Index of help topics:

    AllSitesAboveThreshold
                            Accessor for 'AllSitesAboveThreshold' slot in a
                            'genomicProfileParameters' object.
    BPFrequency             Accessor method for 'BPFrequency' slot in a
                            'genomicProfileParameters' object.
    BPFrequency<-           Setter method for 'BPFrequency' slot in a
                            'genomicProfileParameters' object.
    ChIPanalyser            ChIPanalyser: Predicting Transcription Factor
                            Binding Sites
    ChIPanalyserData        ChIPanalyserData
    DNASequenceLength       Accessor method for 'DNASequenceLength' slot in
                            a 'genomicProfileParameters'
    DNASequenceLength<-     Setter Method for 'DNASequenceLength' slot in a
                            'genomicProfileParameters' object.
    GRList-class            Class '"GRList"'
    NoAccess                Accessor Method for the 'NoAccess' slot in a
                            'genomicProfileParameters' object.
    PFMFormat               Accesor method for the 'PFMFormat' slot in a
                            'genomicProfileParameters' object
    PFMFormat<-             Setter method for the 'PFMFormat' slot in a
                            'genomicProfileParameters' object
    PWMThreshold            Accessor method for the 'PWMThreshold' slot in
                            a 'genomicProfileParameters' object
    PWMThreshold<-          Setter Method for the 'PWMThreshold' slot in a
                            'genomicProfileParameters' object
    PWMpseudocount          Accessor Method for a 'PWMpseudocount' slot in
                            a 'genomicProfileParameters'
    PWMpseudocount<-        Setter Method for the 'pseudocount' slot in a
                            'genomicProfileParameters' object
    PositionFrequencyMatrix
                            Accessor method for the 'PFM' slot in a
                            'genomicProfileParameters' object
    PositionFrequencyMatrix<-
                            Setter method for the 'PFM' slot in a
                            'genomicProfileParameters' object
    PositionWeightMatrix    Accessor Method for the 'PWM' slot in a
                            'genomicProfileParameters' object
    PositionWeightMatrix<-
                            Setter Method for the 'PositionWeightMatrix'
                            slot in a 'genomicProfileParameters' object
    ScalingFactorPWM        Accessor method for the 'lambda' slot in a
                            'genomicProfileParameters' object
    ScalingFactorPWM<-      Setter method for the 'lambda' slot in a
                            'genomicProfileParameters' object
    averageExpPWMScore      Accessor for 'averageExpPWMScore' slot in a
                            'genomicProfileParameters' object.
    backgroundSignal        Accessor method for the 'backgroundSignal' slot
                            in a 'occupancyProfileParameters' object.
    backgroundSignal<-      Setter method for 'backgroundSignal' slot in a
                            'occupancyProfileParameters'
    boundMolecules          Accessor methods for 'boundMolecules' slot in
                            'occupancyProfileParameters' object.
    boundMolecules<-        Setter method for the 'boundMolecules' slot in
                            a 'occupancyProfileParameters' object.
    chipMean                Accessor method for 'chipMean' slot in a
                            'occupancyProfileParameters' object.
    chipMean<-              Access methods for 'chipMean' slot in
                            'occupancyProfileParameters' object.
    chipSd                  Accessor method for 'chipSd' slot in a
                            'occupancyProfileParameters' object.
    chipSd<-                Setter methods for 'chipSd' slot in a
                            'occupancyProfileParameters' object.
    chipSmooth              Accessor methods for 'chipSmooth' slot in a
                            'occupancyProfileParameters' object.
    chipSmooth<-            Setter method for 'chipSmooth' slot in
                            'occupancyProfileParameters' object.
    computeChipProfile      Computing ChIP-seq like profiles from Occupancy
                            data.
    computeGenomeWidePWMScore
                            Computing genome wide PWM scores.
    computeOccupancy        Compute Occupancy values from PWM Scores based
                            on model.
    computeOptimal          compute Optimal Parameters
    computePWMScore         Compute PWM Scores of sites above threshold.
    genomicProfileParameters
                            Genomic Profile Parameter Object
    genomicProfileParameters-class
                            Class '"genomicProfileParameters"'
    maxPWMScore             Accessor function for 'maxPWMScore' slot in a
                            'genomicProfileParameters' object.
    maxSignal               Accessor method for the 'maxSignal' slot in a
                            'occupancyProfileParameters' object.
    maxSignal<-             Setter method for 'maxSignal' slot in a
                            'occupancyProfileParameters' object.
    minPWMScore             Accessor method the 'minPWMScore' slot in a
                            'genomicProfileParameters' object
    naturalLog              Accessor method the 'naturalLog' slot in a
                            'genomicProfileParameters' object.
    naturalLog<-            Setter method for the 'naturalLog' slot in a
                            'genomicProfileParameters' object.
    noOfSites               Accessor Method for the 'noOfSites' slot in a
                            'genomicProfileParameters' object
    noOfSites<-             Setter Method for the 'noOfSites' slot in a
                            'genomicProfileParameters' object.
    occupancyProfileParameters
                            Occupancy Profile Parameters
    occupancyProfileParameters-class
                            Class '"occupancyProfileParameters"'
    ploidy                  Accessor method for the 'ploidy' slot in a
                            'occupancyProfileParameters' object
    ploidy<-                Setter Method for the 'ploidy' slot in an
                            'occupancyProfileParameters' object
    plotOccupancyProfile    Plot Occupancy Profiles
    plotOptimalHeatMaps     Heat Map of optimal Parameters
    processingChIPseq       Pre-processing ChIP-seq data from UCSC format
                            file
    profileAccuracyEstimate
                            Estimating Accuracy of predicted Profiles
    removeBackground        Accessor Method for the 'removeBackground' slot
                            in a 'occupancyProfileParameters' object
    removeBackground<-      Setter Method for the 'removeBackground' slot
                            in a 'occupancyProfileParameters' object
    searchSites             Searching function for Sites above threshold
                            and predicted ChIP-seq Profiles
    stepSize                Accessor method of the 'stepSize' slot in
                            'occupancyProfileParameters' object
    stepSize<-              Setter Method for the 'stepSize' slot in a
                            'occupancyProfileParameters'
    strandRule              Accessor Method for the 'strandRule' slot in a
                            'genomicProfileParameters' object
    strandRule<-            Setter method for the 'strandRule' slot in a
                            'genomicProfileParameters' object.
    thetaThreshold          Accessor method for the 'thetaThreshold' slot
                            in a 'occupancyProfileParameters' object
    thetaThreshold<-        Setter method the 'thetaThreshold' slot in a
                            'occupancyProfileParameters' object
    whichstrand             Accessor method for the 'whichstrand' slot in a
                            'genomicProfileParameters' object
    whichstrand<-           Setter method for the 'whichstrand' slot in a
                            'genomicProfileParameters' object

### 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)){
        source("https://bioconductor.org/biocLite.R")
        biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
    }
    library(BSgenome.Dmelanogaster.UCSC.dm3)
    DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)
    #Building data objects
    GPP <- genomicProfileParameters(PFM=PFM,BPFrequency=DNASequenceSet)
    OPP <- occupancyProfileParameters()

    # Computing Genome Wide
    GenomeWide <- computeGenomeWidePWMScore(DNASequenceSet = DNASequenceSet,
        genomicProfileParameters = GPP)

    #Compute PWM Scores
    PWMScores <- computePWMScore(DNASequenceSet = DNASequenceSet,
        genomicProfileParameters = GenomeWide,
        setSequence = eveLocus, DNAAccessibility = Access)
    #Compute Occupnacy
    Occupancy <- computeOccupancy(AllSitesPWMScore = PWMScores,
        occupancyProfileParameters = OPP)

    #Compute ChIP profiles
    chipProfile <- computeChipProfile(setSequence = eveLocus,
        occupancy = Occupancy, occupancyProfileParameters = OPP)
    #Estimating accuracy estimate
    AccuracyEstimate <- profileAccuracyEstimate(LocusProfile = eveLocusChip,
        predictedProfile = chipProfile, occupancyProfileParameters = OPP)

[Package ChIPanalyser version 1.2.0 Index]