BSseqTstat-class {bsseq} | R Documentation

## 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 khansen@jhsph.edu

### 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.

[Package bsseq version 1.30.0 Index]