posFreqCon-class {cosmo} | R Documentation

## Class "posFreqCon" ~~~

### Description

This class defines a constraint concerning the lower bound for the proportion of a nucleotide at a particular position of the interval

### Objects from the Class

Objects can be created by calls of the form `new('posFreqCon',`
`pos = ...., # Object of class character`
`nuc = ...., # Object of class character`
`lower = ...., # Object of class numeric`
`)` or by: `makePosFreqCon(`
`pos = ...., # Object of class character`
`nuc = ...., # Object of class character`
`lower = ...., # Object of class numeric`
`)`

### Slots

`pos`:
  Object of class `"numeric"` position in the interval of the nucleotide affected by the constraint
`nuc`:
  Object of class `"character"` nucleotide to which the constraint is applied
`lower`:
  Object of class `"numeric"` lower bound for the nucleotide's frequency

### Methods

No methods defined with class "posFreqCon" in the signature.

### Note

~~further notes~~

### Author(s)

Fabian Gallusser, fgallusser@berkeley.edu

### References

### See Also

`boundCon`, `shapeCon`, `subMotifCon`, `shapeDiffCon`, `palCon` `makeConSet`

### Examples

    set=makeConSet(2,c("B","V"),c(5,NA))
    posCon1=makePosFreqCon("2","A",0.5)
    posCon2=makePosFreqCon("All", "G", 0.3)
    conSet=addCon(set,list(posCon1,posCon2),c(1,2))
    # Because the first nucleotide position frequency constraint applies to
    #a specific position, it can only be applied to the interval of type "B".

[Package cosmo version 1.4.0 Index]