View source: R/computePWMScore.R
computePWMScore | 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(genomicProfiles,DNASequenceSet, loci = NULL, chromatinState = NULL,parameterOptions=NULL,cores=1, verbose = TRUE)
DNASequenceSet |
|
genomicProfiles |
|
loci |
|
parameterOptions |
|
chromatinState |
|
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
genomicProfiles
object.
The profiles
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 <pcnmartin@gmail.com>
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"),"BEAF-32.pfm") #As an example of genome, this example will run on the Drosophila genome if(!require("BSgenome.Dmelanogaster.UCSC.dm6", character.only = TRUE)){ if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm6") } library(BSgenome.Dmelanogaster.UCSC.dm6) DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm6) chip<-processingChIP(chip,top) #Building data objects GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR",BPFrequency=DNASequenceSet) # Computing Genome Wide GenomeWide <- computeGenomeWideScores(DNASequenceSet = DNASequenceSet, genomicProfiles = GPP) #Compute PWM Scores PWMScores <- computePWMScore(DNASequenceSet = DNASequenceSet, genomicProfiles = GenomeWide, loci = chip, chromatinState = Access) PWMScores
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