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