| 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: | 1.9.1 |
| 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<-' ~~
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 <- 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)