intInfo-class {cosmo} | R Documentation

## Class "intInfo" ~~~

### Description

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 from the Class

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"}`
`)`

### Slots

`constraintID`:
  Object of class `"numeric"`, indicating which constraint set the interval is part of
`intervalID`:
  Object of class `"numeric"`, indicating the order of the interval in the constraint set
`type`:
  Object of class `"character"`, the interval type: 'B' for base pairs, 'P' for proportion, or 'V' for variable
`length`:
  Object of class `"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 NA
`prop`:
  Object of class `"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 NA
`boundedCon`:
  Object of class `"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`:
  Object of class `"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`:
  Object of class `"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`:
  Object of class `"call"` stores how the object was created

### Methods

plot
  `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.

### Author(s)

Fabian Gallusser, fgallusser@berkeley.edu

### See Also

`writeConFile`,

[Package cosmo version 1.6.0 Index]