minPWMScore | R Documentation |
minPWMScore
slot in a
genomicProfiles
object
Accessor method the minPWMScore
slot in a
genomicProfiles
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
computeGenomeWideScores
function.
Returns the value assigned to the minPWMScore
slot in a
genomicProfiles
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"),"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)
#Building data objects
GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR")
# Computing Genome Wide
GenomceWide <- computeGenomeWideScores(DNASequenceSet = DNASequenceSet,
genomicProfiles = GPP)
minPWMScore(GenomceWide)
## If used before computeGenomeWidePWMScore, will return NULL
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