constraintSet-class {cosmo} | R Documentation

## Class "constraintSet" ~~~

### Description

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 from the Class

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"}`
`)`

### Slots

`description`:
  Object of class `"character"` a general description of the constraint set
`numIntervals`:
  Object of class `"numeric"` number of intervals the motif was split into
`intervals`:
  Object of class `"list"` a list of objects of class `"intInfo"` each describing the constraints imposed on the individual intervals
`shapeDiffCon`:
  Object of class `"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`:
  Object of class `"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`:
  Object of class `"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`:
  Object of class `"call"` stores how the object was created

### Methods

plot
  `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.
print
  `signature(x = "constraintSet",...)` Prints the constraint set in the standard cosmo format.
show
  `signature(object = "constraintSet")` Prints the constraint set in the standard cosmo format.

### Author(s)

Fabian Gallusser, fgallusser@berkeley.edu

### See Also

`writeConFile`, `constraintSet-class`, `intInfo-class`

[Package cosmo version 1.6.0 Index]