addCon {cosmo}R Documentation

Add constraints to an already existing constraint set

Description

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.

Usage

  addCon(conSet, constraint, int=1) 

Arguments

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.

Details

Value

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.

Author(s)

Fabian Gallusser, fgallusser@berkeley.edu

See Also

boundCon, posFreqCon, shapeCon, subMotifCon, shapeDiffCon, palCon makeBoundCon, makePosFreqCon, makeShapeCon, makeSubMotifCon, makeShapeDiffCon, makePalCon

Examples

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.

[Package cosmo version 1.4.0 Index]