annotation-tools: Annotation Tools

In renozao/xbioc: Extra Base Functions for Bioconductor

Description

The xbioc package contains a few utility functions to facilitate working with Bioconductor annotations, which extends or enhance functions available in packages such as annotate.

Usage

is.annpkg(x)

is.orgpkg(x)

is.anndb(x)

biocann_mapname(annotation, map, all = FALSE)

biocann_pkgname(x, noext = FALSE)

biocann_pkgobject(x)

Arguments

x	an R object, either a character string or an annotation object.
annotation	names of an annotation package, with “.db” suffix or not.
map	name of a map, e.g., “ENTREZID”.
all	logical that indicates if all possible names should be returned, and only the simple concatenation of the annotation package's name without “.db” and the map name.
noext	logical that indicates if returned package names should contain the extension '.db'.

Functions

• is.annpkg: is.annpkg tells if an object is the name of an annotation package.

• is.orgpkg: tells if an object is an organism annotation package.

• is.anndb: tells if an object is an annotation db object such as hgu133a.db.

• biocann_mapname: returns the name of a map in an annotation package.

• biocann_pkgname: returns the name of an annotation package, formated from character strings or extracted from annotation objects.

• biocann_pkgobject: retrieve the AnnotationDb object for an annotation package given as a string. The package does not need to be already loaded but needs to be installed in a library that is in the search path.

Examples

# check annotation pkg name
is.annpkg('aaa.db')
is.annpkg(c('bbb.db', 'ccc.db'))
is.annpkg(c('ddd', 'eee.db'))
# check AnnotationDb object
library(hgu133plus2.db)
is.anndb(hgu133plus2.db)
# build annotation bimap object names
biocann_mapname('hgu133plus2.db', 'ENTREZID')
# '.db' extension is skipped
biocann_mapname('hgu133plus2', 'ENTREZID')
# get all possible map names
biocann_mapname('hgu133plus2.db', 'ENTREZID', all=TRUE)
# annotation package name
biocann_pkgname('aa')
# extract the package name from annotation objects
biocann_pkgname(hgu133plus2.db)
biocann_pkgname(hgu133plus2ENTREZID)

# get AnnotationDb object
biocann_pkgobject('hgu133plus2') # extension can be skipped
# the package needs to be installed
try( biocann_pkgobject('aaa') )

renozao/xbioc documentation built on Sept. 3, 2020, 1:13 a.m.