RnBeads.data {RnBeads} | R Documentation

## RnBeads Annotation Tables

### Description

RnBeads uses sets of annotation tables and mappings (from regions to sites) for each of the supported genomes. The structures for one assembly are stored in a separate dedicated annotation package. The following annotation packages are available in Bioconductor:

RnBeads.hg19

  for `"hg19"`

RnBeads.mm10

  for `"mm10"`

RnBeads.mm9

  for `"mm9"`

RnBeads.rn5

  for `"rn5"`

### Format

`list` of four elements - `"regions"`, `"sites"`, `"controls"` and `"mappings"`. These elements are described below.

`"regions"`

  `list` of `NULL`s; the names of the elements correspond to the built-in region annotation tables. Once the default annotations are loaded, the attribute `"builtin"` is a `logical` vector storing, for each region annotation, whether it is the default (built-in) or custom.

`"sites"`

  `list` of `NULL`s; the names of the elements correspond to the site and probe annotation tables.

`"controls"`

  `list` of `NULL`s; the names of the elements correspond to the control probe annotation tables. The attribute `"sites"` is a `character` vector pointing to the site annotation that encompasses the respective control probes.

`"mappings"`

  `list` of `NULL`s; the names of the elements correspond to the built-in region annotation tables.

### Details

An assembly-specific scaffold is automatically loaded upon initialization of its annotation, that is, by the first valid call to any of the following functions: `rnb.get.chromosomes`, `rnb.get.annotation`, `rnb.set.annotation`, `rnb.get.mapping`, `rnb.annotation.size`. Adding an annotation amounts to attaching its table(s) and mapping structures to the scaffold.

### Author(s)

Yassen Assenov

[Package RnBeads version 1.10.8 Index]