biocann_orgdb: Bioconductor Organism Data and Packages

In renozao/xbioc: Extra Base Functions for Bioconductor

Description

Bioconductor Organism Data and Packages

Usage

biocann_orgdb(organism, optional = FALSE)

biocann_orgdb_pkgname(organism)

Arguments

organism	Organism name (case insensitive). Can be specified using the common name (e.g., mouse), a partial match of the latin name (e.g., Mus musculus), or its abbreviation (e.g., Mm). It can also be a AnnDbBimap object like org.Hs.egSYMBOL2EG. The following organisms are currently supported: human, arabidopsis, bovine, canine, chicken, chimp, malaria, mouse, pig, rat, rhesus, worm, zebrafish
optional	logical that indicates if the function should raise an error if no package is found for the given organism specification (optional=FALSE), or return NA data and throw a warning.

Functions

• biocann_orgdb_pkgname: Returns the organism annotation package for a given organism.

Examples

# list all 
biocann_orgdb()

# common name
biocann_orgdb('human')

# latin name
biocann_orgdb('canis')
# any partial match works
biocann_orgdb('canis lupus')

# abbreviation
biocann_orgdb('Mm')

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