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]