BPFrequency<- {ChIPanalyser} | R Documentation

## Setter method for `BPFrequency` slot in a `genomicProfiles` object.

### Description

Setter method for `BPFrequency` slot in a `genomicProfiles` object. If base pair frequency is unknown, `BPFrequency` will compute base pair frequency from a DNA sequence.

### Usage

    BPFrequency(object)<-value

### Arguments

`object` | `object` is a `genomicProfiles` object.
`value` | `value` can three different objects: 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 `BSgenome` of the organism of interest. The base pair frequency will automatically be computed and updated in `genomicProfiles`. A `DNAStringSet` of the organisme of interest. The base pair frequency will automatically be computed and updated in `genomicProfiles` (Prefered method).

### 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 when building a `genomicProfiles` object. The nature of this sequence can be a`BSgenome` object or a `DNAStringSet`. In order to decrease run time, it is advised to use `DNAStringSet`.

### Value

Returns a `genomicProfiles` object with an updated value for `BPFrequency`.

### 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")
    #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 genomicProfiles object
    GPP <- genomicProfiles(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)

[Package ChIPanalyser version 1.9.1 Index]