methylBaseDB-class {methylKit} | R Documentation

## An S4 class for storing methylation events sampled in multiple experiments as flat file database

### Description

This class is designed to contain methylation information such as coverage, number of methylated bases, etc... The class creates an object that holds methylation information and genomic location as flat file database. The object belonging to this class is produced by `unite` function.

### Slots

`dbpath`:

  path to flat file database(s)

`num.records`:

  number of records (lines) in the object

`sample.ids`:

  character vector for ids of samples in the object

`assembly`:

  name of the genome assembly

`context`:

  context of methylation. Ex: CpG,CpH,CHH, etc

`treatment`:

  treatment vector denoting which samples are test and control

`coverage.index`:

  vector denoting which columns in the data correspond to coverage values

`numCs.index`:

  vector denoting which columns in the data correspond to number of methylatedCs values

`numTs.index`:

  vector denoting which columns in the data correspond to number of unmethylated Cs values

`destranded`:

  logical value. If `TRUE` object is destranded, if `FALSE` it is not.

`resolution`:

  resolution of methylation information, allowed values: 'base' or 'region'

`dbtype`:

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

### Details

`methylBaseDB` class has the same functionality as `methylBase` 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 `methylBaseDB`. Subsetting by `x[i,]` will produce a new `methylBase` 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 `methylBaseDB`: `getData`,`getAssembly`, `getContext`

### Coercion

`methylBaseDB` object can be coerced to: `GRanges` object via `as` function. `methylBase` object via `as` function.

### Examples

    data(methylKit)
    methylBaseDB.obj <- unite(methylRawList.obj,save.db=TRUE,dbdir="methylDB")
    library(GenomicRanges)
    my.gr=as(methylBaseDB.obj,"GRanges")

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

[Package methylKit version 1.6.3 Index]