Scale4C-class: Class '"Scale4C"'

In walter-ca/Scale4C: Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

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")

walter-ca/Scale4C documentation built on May 5, 2019, 9:03 p.m.