| BPFrequency<- {ChIPanalyser} | R Documentation |
BPFrequency slot in a
genomicProfileParameters object.
Setter method for BPFrequency slot in a
genomicProfileParameters object.
If base pair frequency is unknown, BPFrequency will compute base pair
frequency from a DNA sequence.
BPFrequency(object)<-value
object |
|
value |
A vector of length 4 containing the probability of occurrence of each base pair (A,C,G,T) in order. Default value is c(0.25,0.25,0.25,0.25). A A |
Default value is c(0.25,0.25,0.25,0.25)
When generating a Postion Weight Matrix from a Position Frequency Matrix,
the probability of occurrence of each base pair (Base Pair Frequency) is
necessary (as originally described by Gary Stormo). It is possible to
set custom values for BPFrequency with a vector of length 4
containing the probability of occurrence of each base pair (A,C,G,T) in order.
If Base pair frequency is unknown, BPFrequency will compute base pair
frequency from a DNA sequence when building a
genomicProfileParameters object.
The nature of this sequence can be aBSgenome object or a
DNAStringSet. In order to decrease run time,
it is advised to use DNAStringSet.
Returns a genomicProfileParameters object with an updated
value for BPFrequency.
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(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)
# Updating BPFrequency
## !! Note!! BPFrequency is used to compute PWM from PFM
## IF updated after building GPP, then it will not influence PWM
## Advised to build with BPFrequency directly
BPFrequency(GPP) <- DNASequenceSet
BPFrequency(GPP) <- c(0.25,0.25,0.25,0.25)