BSrel-class {BiSeq} | R Documentation |
The BSrel
class is derived from
RangedSummarizedExperiment
and contains a SimpleList
of one
matrix named methLevel
as assays
.
Objects can be created by calls of the form
BSrel(metadata = list(),
rowRanges,
colData = DataFrame(row.names=colnames(methLevel)),
methLevel,
...)
.
However, one will most likely create a BSraw
object when use
readBismark
to load data.
metadata
:An optional list
of arbitrary
content describing the overall experiment.
rowRanges
:Object of class "GRanges"
containing the genome positions of CpG-sites covered by bisulfite
sequencing. WARNING: The accessor for this slot is rowRanges
,
not rowRanges
!
colData
:Object of class "DataFrame"
containing information on variable values of the samples.
assays
:Object of class SimpleList
of a
matrix, named methLevel
containing the methylation levels
(between 0 and 1) per CpG site. The rows represent the CpG sites
in rowRanges
and the columns represent the samples in colData
.
Class "RangedSummarizedExperiment"
, directly.
signature(x = "BSrel")
: Gets the methLevel
slot.
signature(x = "BSrel", value = "matrix")
:
Sets the methLevel
slot.
signature(x = "BSrel", y = "BSrel")
: Combines two
BSrel
objects.
Katja Hebestreit
RangedSummarizedExperiment, BSraw-class
, readBismark
showClass("BSrel") ## How to create a BSrel object by hand: metadata <- list(Sequencer = "Sequencer", Year = "2013") rowRanges <- GRanges(seqnames = "chr1", ranges = IRanges(start = c(1,2,3), end = c(1,2,3))) colData <- DataFrame(group = c("cancer", "control"), row.names = c("sample_1", "sample_2")) methLevel <- matrix(c(rep(0.5, 3), rep(1, 3)), ncol = 2) BSrel(metadata = metadata, rowRanges = rowRanges, colData = colData, methLevel = methLevel) # Or get a BSrel object out of a BSraw object: data(rrbs) rrbs.rel <- rawToRel(rrbs)