DNASequenceLength {ChIPanalyser} | R Documentation |
DNASequenceLength
slot in a
genomicProfileParameters
Accessor method for DNASequenceLength
slot in a
genomicProfileParameters
DNASequenceLength(object)
object |
|
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.
Returns DNASequenceLength
slot in a
genomicProfileParameters
object.
Patrick C. N. Martin <p.martin@essex.ac.uk>
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
#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) # Computing Genome Wide GenomceWide <- computeGenomeWidePWMScore(DNASequenceSet = DNASequenceSet, genomicProfileParameters = GPP) DNASequenceLength(GenomceWide)