| BPFrequency {ChIPanalyser} | R Documentation |
BPFrequency slot in a
genomicProfileParameters object.
Extract or Access BPFrequency slot in a
genomicProfileParameters object.
BPFrequency(object)
object |
|
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. The nature of this sequence can be a
BSgenome or a DNAStringSet.
In order to decrease run time, it is advised to use
DNAStringSet
Returns BPFrequency slot in
genomicProfileParameters object.
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")
# Building genomicProfileParameters object
GPP <- genomicProfileParameters(PFM=PFM)
#Extracting BPFrequency slot
BPFrequency(GPP)