addCon {cosmo} | R Documentation |
Given a constraint set, the addCon command allows to add either interval-specific or global constraints to the constraintSet object. The possible interval-specific constraints are: boundCon (for information content bounding constraints), posFreqCon (for position frequency constraints), and shapeCon (for shape constraints). The possible global constraints are: subMotifCon (when part of the motif is known), palCon (for palindromic constraints) and shapeDiffCon (for information content differences between interval extremities). Each constraint can be built with its associated make-command: makeBoundCon, makePosFreqCon, makeShapeCon, makeSubMotifCon, makePalCon and makeShapeDiffCon.
addCon(conSet, constraint, int=1)
conSet |
an object of class "constraint set" |
constraint |
list of constraints constructed with one of the 6 make constraint commands. The length of the list should be the same as that of the 'int' argument. Instead of a list, this may also be a single constraint. |
int |
vector of the intervals to which the constraints given in the constraint argument should be applied. There should be a one-to-one correspondance between the elements of the list and the interval argument. For global constraints, the value of the interval is of no importance but should be present and numeric. |
The output will be an object of class "constraintSet"
resulting of the addition of the constraints to the original constraint set passed as first argument.
Fabian Gallusser, fgallusser@berkeley.edu
boundCon
, posFreqCon
, shapeCon
, subMotifCon
, shapeDiffCon
, palCon
makeBoundCon
, makePosFreqCon
, makeShapeCon
, makeSubMotifCon
, makeShapeDiffCon
, makePalCon
set=makeConSet(4,c("B","P","V","B"),c(4,50,NA,4)) con1=makeBoundCon(1,2) con2=makePalCon(1,4,0.5) con3=makeSubMotifCon("TATA",0.6) con4=makePosFreqCon("2","A",0.5) con5=makePosFreqCon("All","G",0.4) conSet=addCon(set,list(con1,con2,con3,con4,con5),c(2,NA,NA,1,3)) #Because of the palindromic constraint on intervals 1 and 4, the fourth #interval will inherit the nucleotide position frequency constraint #assigned to the first interval.