searchSites {ChIPanalyser} | R Documentation

## 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 <pm16057@essex.ac.uk>

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

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

      #Compute PWM Scores
      PWMScores <- computePWMScore(genomicProfiles = GenomeWide,
           DNASequenceSet = DNASequenceSet, loci = eveLocus, 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=eveLocus)
      searchSites(chipProfile,ScalingFactor=c(1,4), BoundMolecules = c(1,100),
          Locus="eve")

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

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

[Package ChIPanalyser version 1.12.0 Index]