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 the `genomicProfileParameters`'s `AllSitesAboveThreshold` slot or a list resulting from `computeChipProfile`.

### Usage

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

### Arguments

`Sites` | `Sites` is either a `genomicProfileParameters` object or a list ( result of `computeChipProfile`)
`ScalingFactor` | `ScalingFactor` 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

After PWM Scores and/or occupancy have been computed (see `computePWMScore` and `computeOccupancy`, it is possible to extract and search the `AllSitesAboveThreshold` slot. As this slot may be fairly large it can become difficult to navigate. `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. `searchSites` also works on the result of `computeChipProfile`.

### Value

Returns a list or `GRangesList`.

### 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)){
        source("https://bioconductor.org/biocLite.R")
        biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
        }
    library(BSgenome.Dmelanogaster.UCSC.dm3)
    DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)

    #Building data objects
    GPP <- genomicProfileParameters(PFM=PFM,BPFrequency=DNASequenceSet,
        ScalingFactorPWM=c(1,2,3,4))
    OPP <- occupancyProfileParameters(boundMolecules=c(1,10,100))

    # 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)
    # Search on occupancy
    searchSites(Occupancy,ScalingFactor=c(1,4), BoundMolecules = c(1,100))
    #Compute ChIP profiles
    chipProfile <- computeChipProfile(setSequence = eveLocus,
        occupancy = Occupancy,
        occupancyProfileParameters = OPP)

    ## Search on chipProfile
    searchSites(Occupancy,ScalingFactor=c(1,4), BoundMolecules = c(1,100),
        Locus="eve")

[Package ChIPanalyser version 1.2.0 Index]