searchSites {ChIPanalyser} | R Documentation |
searchSites
is function enabling quick extraction and search for
the genomicProfileParameters
's
AllSitesAboveThreshold
slot or a list resulting from computeChipProfile
.
searchSites(Sites,ScalingFactor="all",BoundMolecules="all", Locus="all")
Sites |
|
ScalingFactor |
|
BoundMolecules |
|
Locus |
|
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
.
Returns a list or GRangesList
.
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)){ 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")