DNASequenceLength<- {ChIPanalyser}R Documentation

Setter Method for DNASequenceLength slot in a genomicProfileParameters object.

Description

Setter Method for DNASequenceLength slot in a genomicProfileParameters object.

Usage

DNASequenceLength(object)<- value

Arguments

object

object is a genomicProfileParameters object.

value

value is a numerical value indicating the length of the DNA used and that will be assigned to DNASequenceLength slot in a genomicProfileParameters.

Details

Although it is possible to manually assign the value of the DNA Length, it is not necessary as this value is computed internally in computeGenomeWidePWMScore.

Value

Returns a genomicProfileParameters object with an updated value for the DNASequenceLength slot.

Author(s)

Patrick C.N. Martin <pm16057@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)){
    source("https://bioconductor.org/biocLite.R")
    biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
    }
library(BSgenome.Dmelanogaster.UCSC.dm3)
DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)

# Building genomicProfileParameters object
GPP <- genomicProfileParameters(PFM=PFM,BPFrequency=DNASequenceSet)
# Setting new value for slot
DNASequenceLength(GPP)<- 1500000
# !! This value is computed internally !!
[Package ChIPanalyser version 1.2.0 Index]