| 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)