methylRaw-class {methylKit} | R Documentation

## 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")

[Package methylKit version 1.18.0 Index]