makePosFreqCon {cosmo} | R Documentation

## Constructing a nucleotide frequency constraint

### Description

This function constructs a texttt{posFreqCon} object representing a constraint on the unknown position weight matrix that requires the frequency of a given nucleotide to be above a given lower bound, either at a single position in a given interval, or on average across the entire interval

### Usage

    makePosFreqCon(pos, nuc, lower)

### Arguments

`pos` | This is either the string `avg`, indicating that the average nucleotide frequency across the interval is bounded from below, or a position in the interval, indicating the nucleotide frequency at that position in the interval is bounded from below.
`nuc` | `character` This is one of `A`, `C`, `G`, `T`, `GC`, `AT`.
`lower` | `numeric` the lower bound on the nucleotide frequency of interest

### Value

An object of class texttt{posFreqCon}.

### Author(s)

Fabian Gallusser, fgallusser@berkeley.edu

### See Also

`boundCon`, `shapeCon`, `subMotifCon`, `posFreqCon`, `shapeDiffCon`, `palCon`

### Examples

    pfc <- makePosFreqCon("avg","GC", 0.75)

[Package cosmo version 1.6.0 Index]