computePWMScore: Compute PWM Scores of sites above threshold.
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

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.

1 2	computePWMScore(genomicProfiles,DNASequenceSet, loci = NULL, chromatinState = NULL,parameterOptions=NULL,cores=1, verbose = TRUE)

`DNASequenceSet`	`DNASequenceSet` is a `DNAStringSet` or a `BSgenome` containing the full sequence of the organism of interest.
`genomicProfiles`	`genomicProfiles` is a `genomicProfiles` object resulting from the `computeGenomeWideScores` function.
`loci`	`loci` is a `GRanges` object containing the Loci of interest or a `ChIPScore` object result of `processingChIP` function.
`parameterOptions`	`parameterOptions` is a `parameterOptions` object containing parameters that you wish to parse/change when computing PWMScores.
`chromatinState`	`chromatinState` is a `GRanges` object sites of accessible DNA or DNA affinity scores.
`cores`	`cores` is the number of cores used to compute PWM Scores.
`verbose`	`verbose` is a logical value indicating if progress messages should be printed or not.

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 <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<e2><80><93>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)
eveLocusChip<-processingChIP(eveLocusChip,eveLocus)
#Building data objects
GPP <- genomicProfiles(PFM=PFM,BPFrequency=DNASequenceSet)


# Computing Genome Wide
GenomeWide <- computeGenomeWideScores(DNASequenceSet = DNASequenceSet,
    genomicProfiles = GPP)

#Compute PWM Scores
PWMScores <- computePWMScore(DNASequenceSet = DNASequenceSet,
    genomicProfiles = GenomeWide,
    loci  = eveLocusChip, chromatinState = Access)
PWMScores