computePWMScore {ChIPanalyser} | R Documentation |
computePWMScore
will compute and extract all sites that exhibit a
PWM Score higher than a threshold.
This threshold (see PWMThreshold
) will determine the percentage
of total sites that should NOT be considered.
computePWMScore(DNASequenceSet, genomicProfileParameters, setSequence = NULL, DNAAccessibility = NULL,cores=1, verbose = TRUE)
DNASequenceSet |
|
genomicProfileParameters |
|
setSequence |
|
DNAAccessibility |
|
cores |
|
verbose |
|
After determining genome wide scores, it is possible to only compute and
extract high affinity sites (in the sense that they have a high PWM Score).
If a PWMThreshold
is not set by user,
the default value is set at 0.7.
This means that 70 % of sites will NOT be selected.
Only the top 30 % will be computed and extracted.
If one is interested in all PWM Scores at a genome wide scale
( or accessible DNA ), this is possible by setting
PWMThreshold
to zero.
computePWMScore
will return a
genomicProfileParameters
object.
The AllSitesAboveThreshold
slot will have been updated.
This slot will now contain a GRangesList
with each element being a GRanges
.
This GRanges will contain postion of each sites
(start, end and strand) and the PWMScore associated to that site.
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) # Computing Genome Wide GenomeWide <- computeGenomeWidePWMScore(DNASequenceSet = DNASequenceSet, genomicProfileParameters = GPP) #Compute PWM Scores PWMScores <- computePWMScore(DNASequenceSet = DNASequenceSet, genomicProfileParameters = GenomeWide, setSequence = eveLocus, DNAAccessibility = Access) PWMScores