posFreqCon-class {cosmo} | R Documentation |
This class defines a constraint concerning the lower bound for the proportion of a nucleotide at a particular position of the interval
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
)
pos
:"numeric"
position in the interval of the nucleotide affected by the constraint nuc
:"character"
nucleotide to which the constraint is applied lower
:"numeric"
lower bound for the nucleotide's frequency No methods defined with class "posFreqCon" in the signature.
~~further notes~~
Fabian Gallusser, fgallusser@berkeley.edu
boundCon
, shapeCon
, subMotifCon
, shapeDiffCon
, palCon
makeConSet
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".