CellMix 1.6

Annotation Tools

Description

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

is.annpkg tells if an object is the name of an 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.

Usage

is.annpkg(x)

is.anndb(x)

biocann_mapname(annotation, map, all = FALSE)

biocann_pkgname(x, noext = FALSE)

biocann_pkgobject(x)

S4 (character)
`revmap`(x, ..., simplify = TRUE)

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'.
simplify
a logical that indicates if the reverse mapping should be returned as a character vector whenever possible (TRUE), i.e. when this mapping is 1:1 -- which can happen even if the original mapping is not 1:1. Otherwise the mapping is returned as a list.
...
extra arguments passed to revmap,list-method.

Methods

  1. revmapsignature(x = "character"): The method revmap for character vectors revert a mapping provided as a named character vector.