BSseqStat-class: Class BSseqStat
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 statistics for smoothed whole-genome bisulfite sequencing data.

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

`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.

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

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.

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 ‘BSseqStat’ objects. You can update old serialized (saved) objects by invoking x <- updateObject(x).

Kasper Daniel Hansen khansen@jhsph.edu

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.