methylDiffDB-class {methylKit} | R Documentation

## An S4 class that holds differential methylation information as flat file database

### Description

This class is designed to hold statistics and locations for differentially methylated regions/bases as flat file database. `calculateDiffMeth` function returns an object with `methylDiffDB` class.

### Slots

`dbpath`:

  path to flat file database(s)

`num.records`:

  number of records (lines) in the object

`sample.ids`

  ids/names of samples in a vector

`assembly`

  a name of genome assembly, such as :hg18,mm9, etc

`context`

  numeric vector identifying which samples are which group

`treatment`

  numeric vector identifying which samples are which group

`destranded`

  logical denoting if methylation inormation is destranded or not

`resolution`

  string either 'base' or 'region' defining the resolution of methylation information

`dbtype`:

  string for type of the flat file database, ex: tabix

### Details

`methylDiffDB` class has the same functionality as `methylDiff` class, but the data is saved in a flat database file and therefore allocates less space in memory.

### Subsetting

In the following code snippets, `x` is a `methylDiffDB`. 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[ .

### Coercion

`methylDiffDB` object can be coerced to: `GRanges` object via `as` function. `methylDiff` object via `as` function.

### 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

### Examples

    data(methylKit)

    methylDiffDB.obj <- calculateDiffMeth(methylBase.obj,save.db=TRUE,dbdir="methylDB")

    library(GenomicRanges)
    my.gr=as(methylDiffDB.obj,"GRanges")

    # remove Database again
    rm(methylDiffDB.obj)
    unlink("methylDB",recursive=TRUE)

[Package methylKit version 1.12.0 Index]