DNASequenceLength<- {ChIPanalyser} | R Documentation |
DNASequenceLength
slot in a
genomicProfileParameters
object.
Setter Method for DNASequenceLength
slot in a
genomicProfileParameters
object.
DNASequenceLength(object)<- value
object |
|
value |
|
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
.
Returns a genomicProfileParameters
object with an
updated value for the DNASequenceLength
slot.
Patrick C.N. Martin <pm16057@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) # Setting new value for slot DNASequenceLength(GPP)<- 1500000 # !! This value is computed internally !!