maxPWMScore: Accessor function for 'maxPWMScore' slot in a...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

Accessor function for maxPWMScore slot in a genomicProfiles object.

1	maxPWMScore(object)

object

object is a genomicProfiles 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 genomicProfiles object after using the computeGenomeWideScores.

Returns the value of assigned to the maxPWMScore 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<e2><80><93>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)){
    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 <- genomicProfiles(PFM=PFM,PFMFormat="raw")

# Computing Genome Wide
GenomeWide <- computeGenomeWideScores(DNASequenceSet = DNASequenceSet,
    genomicProfiles = GPP)
maxPWMScore(GenomeWide)
## If used before computeGenomeWidePWMScore, will return NULL