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

In BiSeq: Processing and analyzing bisulfite sequencing data

Description

The BSraw class is derived from RangedSummarizedExperiment and contains a SimpleList of matrices named methReads and totalReads as assays.

Objects from the Class

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.

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 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.

Extends

Class "RangedSummarizedExperiment", directly.

Methods

totalReads

signature(x = "BSraw"): Gets the totalReads slot.

totalReads<-

signature(x = "BSraw", value = "matrix"): Sets the totalReads slot.

methReads

signature(x = "BSraw"): Gets the methReads slot.

methReads<-

signature(x = "BSraw", value = "matrix"): Sets the methReads slot.

combine

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

Author(s)

Katja Hebestreit

See Also

RangedSummarizedExperiment, BSrel-class, readBismark

Examples

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))

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