Data4Cseq-class: Class "Data4Cseq"
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.