DNASequenceLength {ChIPanalyser} | R Documentation

## Accessor method for `DNASequenceLength` slot in a `genomicProfiles`

### 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 <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

    #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)

[Package ChIPanalyser version 1.9.1 Index]