maxPWMScore {ChIPanalyser} | R Documentation |
maxPWMScore
slot in a
genomicProfileParameters
object.
Accessor function for maxPWMScore
slot in a
genomicProfileParameters
object.
maxPWMScore(object)
object |
|
maxPWMScore
is a numerical value that can be described as the
highest PWM score computed at a genome wide scale.
This value is computed and updated in the
genomicProfileParameters
object after using the
computeGenomeWidePWMScore
.
Returns the value of assigned to the maxPWMScore
slot in a
genomicProfileParameters
object.
Patrick C. N. Martin <p.martin@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.
# Loading data #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) # Computing Genome Wide GenomeWide <- computeGenomeWidePWMScore(DNASequenceSet = DNASequenceSet, genomicProfileParameters = GPP) maxPWMScore(GenomeWide) ## If used before computeGenomeWidePWMScore, will return NULL