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.