constraintSet-class {cosmo} | R Documentation |
An object of class "constraintSet"
regroups all the
constraints one wishes to impose when performing detection. The object
consits essentially of constraints on the motif broken down into
seperate intervals, objects of class "intInfo"
Objects can be created by calls of the form
new('constraintSet',
description = ...., # Object of class \code{"character"}
numIntervals = ...., # Object of class \code{"numeric"}
intervals = ...., # Object of class \code{"list"}
shapeDiffCon = ...., # Object of class \code{"data.frame"}
subMotifCon = ...., # Object of class \code{"data.frame"}
palCon = ...., # Object of class \code{"data.frame"}
objectCall = ...., # Object of class \code{"call"}
)
description
:"character"
a general description of the constraint set numIntervals
:"numeric"
number of intervals the motif was split into intervals
:"list"
a list of
objects of class "intInfo"
each describing the constraints
imposed on the individual intervalsshapeDiffCon
:"data.frame"
a
data frame summarizing the global constraints of the shape
constraints. The data frame has four columns: the first two
columns are the intervals and the extremity subject to the
constraint, the extremity being supplied as 'a' for beginning, and 'b' for
end. The third and fourth column are respectively the lower and
upper bounds on the difference between the interval extremities
considered. For example, if c("1b","2a",-0.2,0.5) were a row in
the data frame, it would indicate that the difference in the information content
between the end of the first interval and the beginning of the
second should be between -0.2 and 0.5.subMotifCon
:"data.frame"
a
data frame specifying the submotif global constraints. The two
columns respectiuvely indicate the submotif of interest and it's
error tolerance. The error is computed as the difference in terms
of frequency between the submotif and the position weight matrix.palCon
:"data.frame"
a data
frame summarizing the palindromic constraints imposed on the
motif: the first two columns indicate the two palindromic
intervals and the third is the error tolerated between the
nucleotide frequencies in both intervals. objectCall
:"call"
stores how
the object was created signature(x = "constraintSet", varLen=4,
propLen=4, plot.IC=TRUE, plot.nucFreq=TRUE)
: Plots the
"constraintSet"
object. varLen and propLen are integers
indicating how wide to make the variable and proportion intervals (1
unit is one base pair).
plot.IC and plot.nucFreq are logicals respectively indicating
whether the IC content and the nucleotide frequencies are to be
drawn on the plot.signature(x = "constraintSet",...)
Prints the
constraint set in the standard cosmo format.signature(object = "constraintSet")
Prints the
constraint set in the standard cosmo format.
Fabian Gallusser, fgallusser@berkeley.edu
writeConFile
,
constraintSet-class
,
intInfo-class