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: 1.14.0
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: RELEASE_3_13
git_last_commit: 68caeca
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19

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 1.14.0 Index]