RnBeads.data {RnBeads} | R Documentation |
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:
for "hg19"
for "mm10"
for "mm9"
for "rn5"
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.
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.
Yassen Assenov