Scale4C-class {Scale4C} | R Documentation

## Class `"Scale4C"`

### Description

This class is a container for information on a specific 4C-seq scale-space transformation. Stored information includes raw read data, the experiment's viewpoint location (optional), possible points of interest, the scale-space fingerprint map, and a list of identified singularities in scale-space.

### Objects from the Class

Objects can be created by calls of the form `new("Scale4C", ...)`.

### Slots

`viewpoint`:

  Object of class `"numeric"` representing the viewpoint's location

`viewpointChromosome`:

  Object of class `"character"` representing the viewpoint's chromosome

`pointsOfInterest`:

  Object of class `"GRanges"` representing any points of interest to be marked in the visualizations (usually near-cis based, i.e. close to the viewpoint)

`rawData`:

  Object of class `"GRanges"` representing the 4C-seq reads (or signal strength) of the experiment at given genomic positions

`scaleSpace`:

  Object of class `"SummarizedExperiment"` representing the gradually smoothed 4C-seq signal ('scale space') in its first assay and the corresponding fingerprint map in its second assay.

`singularities`:

  Object of class `"GRanges"` representing singularities in the fingerprint map for the given 4C-seq signal

### Methods

viewpoint<-

  `signature(object = "Scale4C", value = "numeric")`: Setter-method for the viewpoint slot.

viewpoint

  `signature(object = "Scale4C")`: Getter-method for the viewpoint slot.

viewpointChromosome<-

  `signature(object = "Scale4C", value = "character")`: Setter-method for the viewpointChromosome slot.

viewpointChromosome

  `signature(object = "Scale4C")`: Getter-method for the viewpointChromosome slot.

pointsOfInterest<-

  `signature(object = "Scale4C", value = "GRanges")`: Setter-method for the pointsOfInterest slot.

pointsOfInterest

  `signature(object = "Scale4C")`: Getter-method for the pointsOfInterest slot.

rawData<-

  `signature(object = "Scale4C", value = "GRanges")`: Setter-method for the rawData slot.

rawData

  `signature(object = "Scale4C")`: Getter-method for the rawData slot.

scaleSpace<-

  `signature(object = "Scale4C", value = "matrix")`: Setter-method for the scaleSpace slot.

scaleSpace

  `signature(object = "Scale4C")`: Getter-method for the scaleSpace slot.

singularities<-

  `signature(object = "Scale4C", value = "GRanges")`: Setter-method for the singularities slot.

singularities

  `signature(object = "Scale4C")`: Getter-method for the singularities slot.

### Author(s)

Carolin Walter

### Examples

        showClass("Scale4C")

[Package Scale4C version 1.6.0 Index]