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]