intInfo-class {cosmo} | R Documentation |
An object of class "intInfo"
contains all the
constraints one wishes to impose on an interval of the motif.
Combined "intInfo"
objects will constitue an object of class
"constraintSet"
Objects can be created by calls of the form
new('intInfo',
constraintID = ...., # Object of class \code{"numeric"}
intervalID = ...., # Object of class \code{"numeric"}
type = ...., # Object of class \code{"character"}
length = ...., # Object of class \code{"numeric"}
prop = ...., # Object of class \code{"numeric"}
boundedCon = ...., # Object of class \code{"data.frame"}
posFreqConCon = ...., # Object of class \code{"data.frame"}
shapeCon = ...., # Object of class \code{"data.frame"}
objectCall = ...., # Object of class \code{"call"}
)
constraintID
:"numeric"
,
indicating which constraint set the interval is part ofintervalID
:"numeric"
,
indicating the order of the interval in the constraint settype
:"character"
, the interval
type: 'B' for base pairs, 'P' for proportion, or 'V' for variablelength
:"numeric"
, the length
of the interval: if the interval is of type 'B', the length is the
number of base pairs, if the
interval is of type 'P' or 'V', this slot is NAprop
:"numeric"
, the ratio of
the interval lengtb to the total motif width. This slot is only
defined for intervals of type 'P', in which case
the value is between 0 and 100%. For intervals of type 'B' or
'V', this slot is NAboundedCon
:"data.frame"
a data
frame summarizing the information content bounding constraints on
the interval: the first column indicates the position of the
interval among the intervals constituing the constraint set, the
second and third column are respetively the lower and upper bound
of the information content on the interval.posFreqCon
:"data.frame"
a data
frame summarizing the position nucleotide frequency constraints
imposed on the interval: the first column indicates the interval
to which the constraint is applied, the second column the position
concerned ('All' cab be specified if the constraint applies to the
entire interval). It is to be noted that a specific position mat
only be specified if the interval is of type 'B'. The third column
is the nucleotide concerned, either A, C, G, T, AT, or GC are
accepted at this time. Finally the fourth column indicates the
lower bound for the given nucleotide at the given position. shapeCon
:"data.frame"
a data
frame summarizing the shape constraint on the interval. The first
column indicates the interval to which the constraint is applied,
the second the shape of the variation either 'linear', 'monotone
decreasing', or 'monotone increasing'. The third and fourth column
(respectively fifth and sixth) record the lower and upper bounds
of the information content at the beginning (respectively end) of
the interval. Finally, the seventh column records the error
tolerated.objectCall
:"call"
stores how
the object was created signature(x = "intInfo", varLen=4, propLen=4,
plot.IC=TRUE, plot.nucFreq=TRUE)
: plots the "intInfo"
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.
Fabian Gallusser, fgallusser@berkeley.edu