methylRaw-class: An S4 class for holding raw methylation data from an...

In al2na/methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results

An S4 class for holding raw methylation data from an alignment pipeline.

Description

This object stores the raw mehylation data that is read in through read function and extends data.frame.The raw methylation data is basically percent methylation values and read coverage values per genomic base/region.

Slots

sample.id:

string for an identifier of the sample

assembly:

string for genome assembly, ex: hg18,hg19,mm9

context:

methylation context string, ex: CpG,CpH,CHH, etc.

resolution:

resolution of methylation information, 'base' or 'region'

Details

methylRaw class extends data.frame class therefore providing novice and experienced R users with a data structure that is well known and ubiquitous in many R packages.

Subsetting

In the following code snippets, x is a methylRaw. Subsetting by x[i,] will produce a new object if subsetting is done on rows. Column subsetting is not directly allowed to prevent errors in the downstream analysis. see ?methylKit[ .

Accessors

The following functions provides access to data slots of methylDiffDB: - getData: get the data slot from the methylKit objects, - getAssembly: get assembly of the genome, - getContext: get the context of methylation

Coercion

methylRaw object can be coerced to GRanges object via as function.

Examples

# example of a raw methylation data as a text file
read.table(system.file("extdata", "control1.myCpG.txt", 
                                package = "methylKit"),
                                    header=TRUE,nrows=5)

data(methylKit)

# example of a methylRaw object
head(methylRawList.obj[[1]])
str(head(methylRawList.obj[[1]]))

library(GenomicRanges)

#coercing methylRaw object to GRanges object
my.gr=as(methylRawList.obj[[1]],"GRanges")

al2na/methylKit documentation built on Feb. 1, 2024, 4:42 p.m.