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 NULLs; 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 NULLs; the names of the elements correspond to the site and probe annotation tables.

"controls"

list of NULLs; 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 NULLs; 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