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)){ 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 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)