BSseqTstat-class: Class BSseqTstat

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

Class BSseqTstat

Description

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

Usage

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

Arguments

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

Details

The 'stats' matrix-like object will be coerced to a DelayedMatrix object; 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 BSseqTstat(...). However, usually objects are returned by BSmooth.tstat(...) and not constructed by the user..

Slots

stats:

This is a DelayedMatrix object with columns representing various statistics for methylation loci along the genome.

parameters:

Object of class list. A list of parameters representing how the t-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 ‘BSseqTstat’ objects. You can update old serialized (saved) objects by invoking x <- updateObject(x).

Author(s)

Kasper Daniel Hansen [e-mail]

See Also

The package vignette(s). hasGRanges for accessing the genomic locations. BSmooth.tstat for a function that returns objects of class BSseqTstat, and dmrFinder for a function that computes DMRs based on the t-statistics. Also see BS.cancer.ex.tstat for an example of the class in the bsseqData package.

Examples

if(require(bsseqData)) {
    data(BS.cancer.ex.tstat)
    dmrFinder(BS.cancer.ex.tstat)
}

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