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

maxPWMScore

R Documentation

Accessor function for `maxPWMScore` slot in a `genomicProfiles` object.

Description

Accessor function for maxPWMScore slot in a genomicProfiles object.

Usage

maxPWMScore(object)

Arguments

object

object is a genomicProfiles object.

Details

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.

Value

Returns the value of assigned to the maxPWMScore slot in a genomicProfiles object.

Author(s)

Patrick C. N. Martin <p.martin@essex.ac.uk>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

Examples


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

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.