ChIPanalyser-package: ChIPanalyser: Predicting Transcription Factor Binding Sites

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPanalyser: Predicting Transcription Factor Binding Sites

Description

ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.

Details

The DESCRIPTION file: This package was not yet installed at build time.
Index: This package was not yet installed at build time.

Author(s)

Patrick C.N. Martin <[e-mail]>

And

Nicolae Radu Zabet <[e-mail]>

Maintainer: Patrick C.N. Martin <[e-mail]>

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"),"BEAF-32.pfm")
#As an example of genome, this example will run on the Drosophila genome

if(!require("BSgenome.Dmelanogaster.UCSC.dm6", character.only = TRUE)){
    if (!requireNamespace("BiocManager", quietly=TRUE))
        install.packages("BiocManager")
    BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm6")
}
library(BSgenome.Dmelanogaster.UCSC.dm6)
DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm6)
#Building data objects
GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR",BPFrequency=DNASequenceSet)

chip<-processingChIP(chip,top)
# Computing Genome Wide
GenomeWide <- computeGenomeWideScores(DNASequenceSet = DNASequenceSet,
    genomicsProfiles = GPP)

#Compute PWM Scores
PWMScores <- computePWMScore(genomicsProfiles = GenomeWide,
    DNASequenceSet = DNASequenceSet,
    loci = top, chromatinState = Access)
#Compute Occupnacy
Occupancy <- computeOccupancy(genomicsProfiles = PWMScores,
    parameterOptions = OPP)

#Compute ChIP profiles
chipProfile <- computeChIPProfile(genomicProfiles = Occupancy,
     loci = top,
    parameterOptions = OPP)
#Estimating accuracy estimate
AccuracyEstimate <- profileAccuracyEstimate(genomicProfiles = chipProfile,
     ChIPScore = chip,
     parameterOptions = OPP)

    

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.