Data4Cseq-class: Class '"Data4Cseq"'

In Basic4Cseq: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Description

This class is a container for information on a specific 4C-seq experiment. Stored information includes raw reads, fragment data, and the experiment's viewpoint location.

Objects from the Class

Objects can be created by calls of the form new("Data4Cseq", ...).

Slots

viewpointChromosome:

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

viewpointInterval:

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

readLength:

Object of class "numeric" representing the experiment's read length

pointsOfInterest:

Object of class "data.frame" representing any points of interest to be marked in the near-cis visualizations

rawReads:

Object of class "GAlignments" representing the raw 4C-seq reads of the experiment

rawFragments:

Object of class "data.frame" representing the experiment's corresponding virtual fragment library

nearCisFragments:

Object of class "data.frame" representing near-cis data in fragment form

Methods

viewpointChromosome<-

signature(object = "Data4Cseq", value = "character"): Setter-method for the viewpointChromosome slot.

viewpointChromosome

signature(object = "Data4Cseq"): Getter-method for the viewpointChromosome slot.

viewpointInterval<-

signature(object = "Data4Cseq", value = "numeric"): Setter-method for the viewpointInterval slot.

viewpointInterval

signature(object = "Data4Cseq"): Getter-method for the viewpointInterval slot.

readLength<-

signature(object = "Data4Cseq", value = "numeric"): Setter-method for the readLength slot.

readLength

signature(object = "Data4Cseq"): Getter-method for the readLength slot.

pointsOfInterest<-

signature(object = "Data4Cseq", value = "data.frame"): Setter-method for the pointsOfInterest slot.

pointsOfInterest

signature(object = "Data4Cseq"): Getter-method for the pointsOfInterest slot.

rawReads<-

signature(object = "Data4Cseq", value = "GAlignments"): Setter-method for the rawReads slot.

rawReads

signature(object = "Data4Cseq"): Getter-method for the rawReads slot.

rawFragments<-

signature(object = "Data4Cseq", value = "data.frame"): Setter-method for the rawFragments slot.

rawFragments

signature(object = "Data4Cseq"): Getter-method for the rawFragments slot.

nearCisFragments<-

signature(object = "Data4Cseq", value = "data.frame"): Setter-method for the nearCisFragments slot.

nearCisFragments

signature(object = "Data4Cseq"): Getter-method for the nearCisFragments slot.

Author(s)

Carolin Walter

Examples

showClass("Data4Cseq")

Basic4Cseq documentation built on Nov. 8, 2020, 6:53 p.m.