searchSites {ChIPanalyser} | R Documentation |
searchSites
is function enabling quick extraction and search for
parameter combinations and/or loci in any genomicProfiles
object
from computeOccupancy onwards.
searchSites(Sites,lambdaPWM="all",BoundMolecules="all", Locus="all")
Sites |
|
lambdaPWM |
|
BoundMolecules |
|
Locus |
|
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
.
Returns object of same time as parsed to this function with only the parameters and/or loci selected.
Patrick C. N. Martin <pm16057@essex.ac.uk>
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
#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")