DNASequenceLength: Accessor method for 'DNASequenceLength' slot in a...

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

Description

Accessor method for DNASequenceLength slot in a genomicProfiles

Usage

DNASequenceLength(object)

Arguments

object

object is a genomicProfiles

Details

The model on which is based ChIPanalyser requires the length of the DNA sequence used to compute scores. In this circustance, this DNA Length is the total length of the DNA of the organism of interest or the the Accessible DNA at a genome wide scale.

Value

Returns DNASequenceLength 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 genomicProfiles object
GPP <- genomicProfiles(PFM=PFM,BPFrequency=DNASequenceSet)
# Computing Genome Wide
GenomceWide <- computeGenomeWideScores(DNASequenceSet = DNASequenceSet,
    genomicProfiles = GPP)

DNASequenceLength(GenomceWide)

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