BSraw-class {BiSeq} | R Documentation |
The BSraw
class is derived from
RangedSummarizedExperiment
and contains a SimpleList
of
matrices named methReads
and totalReads
as assays
.
Objects can be created by calls of the form
BSraw(metadata = list(),
rowRanges,
colData = DataFrame(row.names=colnames(methReads)),
methReads,
totalReads,
...)
.
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 two
matrices, named totalReads
and methReads
. The matrix
totalReads
contains the number of reads spanning a
CpG-site. The rows represent the CpG sites in rowRanges
and
the columns represent the samples in colData
. The matrix
methReads
contains the number of methylated reads spanning
a CpG-site.
Class "RangedSummarizedExperiment"
, directly.
signature(x = "BSraw")
: Gets the totalReads
slot.
signature(x = "BSraw", value = "matrix")
:
Sets the totalReads
slot.
signature(x = "BSraw")
: Gets the methReads
slot.
signature(x = "BSraw", value = "matrix")
:
Sets the methReads
slot.
signature(x = "BSraw", y = "BSraw")
: Combines two
BSraw
objects.
Katja Hebestreit
RangedSummarizedExperiment, BSrel-class
, readBismark
showClass("BSraw") ## How to create a BSraw 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")) totalReads <- matrix(c(rep(10L, 3), rep(5L, 3)), ncol = 2) methReads <- matrix(c(rep(5L, 3), rep(5L, 3)), ncol = 2) BSraw(metadata = metadata, rowRanges = rowRanges, colData = colData, totalReads = totalReads, methReads = methReads) ## A more realistic example can be loaded: data(rrbs) rrbs head(totalReads(rrbs)) head(methReads(rrbs))