BPFrequency {ChIPanalyser} | R Documentation

## Accessor method for `BPFrequency` slot in a `genomicProfileParameters` object.

### Description

Extract or Access `BPFrequency` slot in a `genomicProfileParameters` object.

### Usage

    BPFrequency(object)

### Arguments

`object` | `object` is a `genomicProfileParameters`

### Details

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`

### Value

Returns `BPFrequency` slot in `genomicProfileParameters` object.

### Author(s)

Patrick C.N. Martin <pm16057@essex.ac.uk>

### References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

### Examples

    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)

[Package ChIPanalyser version 1.2.0 Index]