BSrel-class: Class to contain Bisulfite Sequencing (BiSeq) Data

In BiSeq: Processing and analyzing bisulfite sequencing data

Description

The BSrel class is derived from RangedSummarizedExperiment and contains a SimpleList of one matrix named methLevel as assays.

Objects from the Class

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.

Slots

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.

Extends

Class "RangedSummarizedExperiment", directly.

Methods

methLevel

signature(x = "BSrel"): Gets the methLevel slot.

methLevel<-

signature(x = "BSrel", value = "matrix"): Sets the methLevel slot.

combine

signature(x = "BSrel", y = "BSrel"): Combines two BSrel objects.

Author(s)

Katja Hebestreit

See Also

RangedSummarizedExperiment, BSraw-class, readBismark

Examples

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)

BiSeq documentation built on Nov. 8, 2020, 8:05 p.m.