searchSites: Searching function for Sites above threshold and predicted...

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

Searching function for Sites above threshold and predicted ChIP-seq Profiles

Description

searchSites is function enabling quick extraction and search for parameter combinations and/or loci in any genomicProfiles object from computeOccupancy onwards.

Usage

searchSites(Sites,lambdaPWM="all",BoundMolecules="all", Locus="all")

Arguments

Sites	Sites is either a genomicProfiles or the result of computeOptimal
lambdaPWM	lambdaPWM is a numeric vector describing the ScalingFactors that should be searched within Sites.
BoundMolecules	BoundMolecules is a numeric vector describing the BoundMolecules that should be searched within Sites.
Locus	Locus is a character vector describing the Loci that should be searched within Sites.

Details

When testing numerous combinations of lambdaPWM and boundMolecules on top of many loci, it can become challenging to navigate the large data output searchSites will make searching in this slot a lot easier. If all arguments are left at their default value of "all", then all Parameters will be searched thus returning the full list of Sites above threshold. If a value for lambdaPWM is user provided then only this lambdaPWM will be selected (all boundMolecules and loci will also be selected). searchSites also works on the result of computeOptimal.

Value

Returns object of same time as parsed to this function with only the parameters and/or loci selected.

Author(s)

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. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

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 genomicProfiles object
  GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR", BPFrequency=DNASequenceSet)


  # Computing Genome Wide
  GenomeWide <- computeGenomeWideScore(genomicProfiles = GPP,
      DNASequenceSet = DNASequenceSet)

  #Compute PWM Scores
  PWMScores <- computePWMScore(genomicProfiles = GenomeWide,
       DNASequenceSet = DNASequenceSet, loci = top, chromatinState = Access)
  #Compute Occupnacy
  Occupancy <- computeOccupancy(genomicProfiles = PWMScores)
  searchSites(Occupancy,ScalingFactor=c(1,4), BoundMolecules = c(1,100),
      Locus="eve")

  #Compute ChIP profiles
  chipProfile <- computeChIPProfile(genomicProfiles=Occupancy,loci=top)
  searchSites(chipProfile,ScalingFactor=c(1,4), BoundMolecules = c(1,100),
      Locus="eve")

optimalParam <- computeOptimal(genomicProfiles = GPP,
        DNASequenceSet = DNASequenceSet,
        ChIPScore = chip,
        chromatinState = Access,
        parameterOptions = OPP,
        parameter = "all",
        peakMethod="moving_kernel")

searchSites(optimalParam,ScalingFactor=c(1,4), BoundMolecules = c(1,100),
    Locus="eve")

patrickCNMartin/ChIPanalyser documentation built on Nov. 24, 2022, 12:02 a.m.