hasGRanges-class: Class hasGRanges
In kasperdanielhansen/bsseq: Analyze, manage and store whole-genome methylation data

hasGRanges-class

R Documentation

Class hasGRanges

Description

A class with a GRanges slot, used as a building block for other classes. Provides basic accessor functions etc.

Objects from the Class

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

Slots

gr:: Object of class GRanges.

Methods

"[": Subsets a single dimension.
granges: Get the GRanges object representing genomic locations.
start,start<-,end,end<-,width,width<-: Start, end and width for the genomic locations of the object, also replacement functions. This accessor functions operate directly on the gr slot.
strand,strand<-: Getting and setting the strand of the genomic locations (the gr slot).
seqlengths,seqlengths<-: Getting and setting the seqlengths of the genomic locations (the gr slot).
seqlevels,seqlevels<-: Getting and setting the seqlevels of the genomic locations (the gr slot).
seqnames,seqnames<-: Getting and setting the seqnames of the genomic locations (the gr slot).
show: The show method.
findOverlaps: (query = "hasGRanges", subject = "hasGRanges"): finds overlaps between the granges() of the two objects.
findOverlaps: (query = "GenomicRanges", subject = "hasGRanges"): finds overlaps between query and the granges() of the subject.
findOverlaps: (query = "hasGRanges", subject = "GenomicRanges"): finds overlaps between the granges() of the query and the subject.
subsetByOverlaps: (query = "hasGRanges", subject = "hasGRanges"): Subset the query, keeping the genomic locations that overlaps the subject.
subsetByOverlaps: (query = "hasGRanges", subject = "GenomicRanges"): Subset the query, keeping the genomic locations that overlaps the subject.
subsetByOverlaps: (query = "GenomicRanges", subject = "hasGRanges"): Subset the query, keeping the genomic locations that overlaps the subject.

Note

If you extend the hasGRanges class, you should consider writing a subset method ([), and a show method. If the new class supports single index subsetting, the subsetByOverlaps methods will automatically extend.