ChIPanalyser-package {ChIPanalyser} | R Documentation |
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.
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: | 1.4.0 |
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 (>= 3.5.1),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_8 |
git_last_commit: | b5a2283 |
git_last_commit_date: | 2018-10-30 |
Date/Publication: | 2018-10-30 |
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
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>
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
#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)