BSseqTstat-class: Class BSseqTstat
In bsseq: Analyze, manage and store bisulfite sequencing data

Description Usage Arguments Details Objects from the Class Slots Extends Methods Utilities Coercion Author(s) See Also

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

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

`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.

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

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.

Class hasGRanges, directly.

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

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.

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).

Kasper Daniel Hansen khansen@jhsph.edu

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.