| BSseqTstat-class {bsseq} | R Documentation |
A class for representing t-statistics for smoothed whole-genome bisulfite sequencing data.
BSseqTstat(gr = NULL, stats = NULL, parameters = NULL)
gr |
The genomic locations as an object of class |
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.
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.