BSseqStat-class: Class BSseqStat

In hansenlab/bsseq: Analyze, manage and store whole-genome methylation data

Class BSseqStat

Description

A class for representing statistics for smoothed whole-genome bisulfite sequencing data.

Usage

    BSseqStat(gr = NULL, stats = NULL, parameters = NULL)

Arguments

gr	The genomic locations as an object of class GRanges.
stats	The statistics, as a list of matrix-like objects (see 'Details' below).
parameters	A list of parameters.

Details

The matrix-like elements of the list in the 'stats' slot will be coerced to DelayedMatrix objects; see ?DelayedArray::DelayedMatrix for the full list of supported matrix-like objects. We recommend using matrix objects for in-memory storage of data and HDF5Matrix for on-disk storage of data.

Objects from the Class

Objects can be created by calls of the form BSseqStat(...). However, usually objects are returned by BSmooth.fstat(...) and not constructed by the user.

Slots

stats:

This is a list of DelayedMatrix objects with list elements representing various statistics for methylation loci along the genome.

parameters:

Object of class list. A list of parameters representing how the statistics were computed.

gr:

Object of class GRanges giving genomic locations.

Extends

Class hasGRanges, directly.

Methods

[

The subsetting operator; one may only subset in one dimension, corresponding to methylation loci.

show

The show method.

Utilities

This class extends hasGRanges and therefore inherits a number of useful GRanges methods that operate on the gr slot, used for accessing and setting the genomic locations and also do subsetByOverlaps.

Coercion

Package version 1.11.1 introduced a new version of representing ‘BSseqStat’ objects. You can update old serialized (saved) objects by invoking x <- updateObject(x).

Author(s)

Kasper Daniel Hansen [e-mail]

See Also

hasGRanges for accessing the genomic locations. BSmooth.fstat for a function that returns objects of class BSseqStat, and smoothSds, computeStat and dmrFinder for functions that operate based on these statistics. Also see the more specialised BSseqTstat.

hansenlab/bsseq documentation built on Dec. 17, 2024, 1:33 a.m.