getBackgroundFrequencies {PWMEnrich} | R Documentation

## Get the four nucleotides background frequencies

### Description

Estimate the background frequencies of A,C,G,T on a set of promoters from an organism

### Usage

      getBackgroundFrequencies(organism = "dm3",
        pseudo.count = 1, quick = FALSE)

### Arguments

`organism` | either a name of the organisms for which the background should be compiled (supported names are "dm3", "mm9" and "hg19"), a `BSgenome` object, `DNAStringSet`, or list of `DNAString` objects
`pseudo.count` | the number to which the frequencies sum up to, by default 1
`quick` | if to preform fitting on a reduced set of 100 promoters. This will not give as good results but is much quicker than fitting to all the promoters (~10k). Usage of this parameter is recommended only for testing and rough estimates.

### Author(s)

Robert Stojnic, Diego Diez

### Examples

    ## Not run:
      getBackgroundFrequencies("dm3")

    ## End(Not run)

[Package PWMEnrich version 4.20.0 Index]