computeChIPProfile {ChIPanalyser} | R Documentation |
computeChIPProfile
compute ChIP-seq like profile from occupancy data.
Occupancy data is computed using computeOccupancy
.
computeChIPProfile(genomicProfiles, loci, parameterOptions = NULL, norm = TRUE, method = c("moving_kernel","truncated_kernel","exact"), peakSignificantThreshold= NULL,cores=1, verbose = TRUE)
genomicProfiles |
|
loci |
|
parameterOptions |
|
norm |
|
method |
|
peakSignificantThreshold |
|
cores |
|
verbose |
|
computeChIPProfile
converts Transcription Factor occuapncy to a profile
resembling the one of a ChIP-seq profile. Internally a few paramters are required
to build a ChIP like profile. These parameters are either defined and stored in
a ChIPScore
object (Paramters are updated based on
your ChIP data ), a genomicProfiles
(user defined at the
start of the analysis) or a parameterOptions
(if you want to
update values as you go along)
Returns a genomicProfiles
objec containing all ChIP-seq like
profile for every combination of lambdaPWM
and boundMolecules
provided by the user.
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.
#Extracting Data 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, PFMFormat="raw",BPFrequency=DNASequenceSet) # Computing Genome Wide GenomeWide <- computeGenomeWideScores(genomicProfiles = GPP, DNASequenceSet = DNASequenceSet) #Compute PWM Scores PWMScores <- computePWMScore(genomicProfiles = GenomeWide, DNASequenceSet = DNASequenceSet, loci = eveLocus, chromatinState = Access) #Compute Occupnacy Occupancy <- computeOccupancy(genomicProfiles = PWMScores) #Compute ChIP profiles chipProfile <- computeChIPProfile(genomicProfiles=Occupancy,loci=eveLocus) chipProfile