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: 1.6.0
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 genomeWidePWM.R parallelInternalFunctions.R GenomicProfileGenericFunctions.R plotOccupancyDev.R plotOptimalHeatMapDev.R DataPreprocessing.R DataPreprocessingGenericFunctions.R profileAccuracyEstimate.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_9
git_last_commit: 750b092
git_last_commit_date: 2019-05-02
Date/Publication: 2019-05-02

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.
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)){
    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 <- 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 1.6.0 Index]