minPWMScore: Accessor method the 'minPWMScore' slot in a 'genomicProfiles'...

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

Description

Accessor method the minPWMScore slot in a genomicProfiles object

Usage

minPWMScore(object)

Arguments

object

object is a genomicProfiles object.

Details

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.

Value

Returns the value assigned to the minPWMScore 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

#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
GenomceWide <- computeGenomeWideScores(DNASequenceSet = DNASequenceSet,
    genomicProfiles = GPP)
minPWMScore(GenomceWide)

## If used before computeGenomeWidePWMScore, will return NULL

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