hasGRanges-class: Class hasGRanges

In bsseq: Analyze, manage and store bisulfite sequencing data

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.

Author(s)

Kasper Daniel Hansen [e-mail]

Examples

showClass("hasGRanges")

bsseq documentation built on Nov. 8, 2020, 7:53 p.m.