maxPWMScore: Accessor function for 'maxPWMScore' slot in a...

In patrickCNMartin/ChIPanalyserDev: ChIPanalyser: Predicting Transcription Factor Binding Sites

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 <[e-mail]>

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"),"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

patrickCNMartin/ChIPanalyserDev documentation built on Nov. 14, 2019, 4:39 p.m.