minPWMScore {ChIPanalyser} | R Documentation |
minPWMScore
slot in a
genomicProfileParameters
object
Accessor method the minPWMScore
slot in a
genomicProfileParameters
object
minPWMScore(object)
object |
|
minPWMScore
can be described as the lowest PWM score computed at
a genome wide scale. Although it is possible to assigne a value
to minPWMScore
, we strongly advise to use the value
computed and assigned internally. This value is computed in the
computeGenomeWidePWMScore
function.
Returns the value assigned to the minPWMScore
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.
#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) #Building data objects GPP <- genomicProfileParameters(PFM=PFM) # Computing Genome Wide GenomceWide <- computeGenomeWidePWMScore(DNASequenceSet = DNASequenceSet, genomicProfileParameters = GPP) minPWMScore(GenomceWide) ## If used before computeGenomeWidePWMScore, will return NULL