biocann_object. CellMix 1.6

Description

The function biocann_object retrieves annotation objects, like bimaps, from Bioconductor annotation packages. It is similar to the function getAnnMap from the annotate package, except that it also accepts annotation -- bimap -- objects, and will try to install missing packages if not found (see section Details).

Usage

biocann_object(to, from = NULL, optional = FALSE)

Arguments

to: target annotation field as a character string, e.g., “ENTREZID”, “ENSEMBL”, or an annotation package or db which means that one wants to retrieve a mapping to its corresponding primary identifier. If from is missing, to must be the name of an annotation package, i.e. ends with “db”), in which case it tries loading the package and return the whole annotation db object; or any annotation package db or map object such as AnnDbBimap, ChipDb or OrgDb objects, which are returned unchanged.
from: source annotation package as a character string e.g. "hgu133a.db".
optional: logical that indicates if the function should return NULL if the mapping cannot be found (TRUE), or throw an error. Note that this does not apply to the installation part: if a required annotation package is missing, an error is thrown even if optional=TRUE.

Value

a ProbeAnnDbBimap if annotation is not missing, a ProbeAnnDb object otherwise.

Details

If an annotation package is specified as a character string, and is not found in the search path, and if R runs in interactive mode, then the user is asked whether one should try install the missing package. Default response is 'yes' so that simply hitting return will install the package via install.packages and load it. An error is thrown if this eventually fails.

Examples


# db package object
biocann_object('hgu133a.db')

## ChipDb object:
## | DBSCHEMAVERSION: 2.1
## | Db type: ChipDb
## | Supporting package: AnnotationDbi
## | DBSCHEMA: HUMANCHIP_DB
## | ORGANISM: Homo sapiens
## | SPECIES: Human
## | MANUFACTURER: Affymetrix
## | CHIPNAME: Human Genome U133 Set
## | MANUFACTURERURL: http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133
## | EGSOURCEDATE: 2013-Mar5
## | EGSOURCENAME: Entrez Gene
## | EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
## | CENTRALID: ENTREZID
## | TAXID: 9606
## | GOSOURCENAME: Gene Ontology
## | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
## | GOSOURCEDATE: 20130302
## | GOEGSOURCEDATE: 2013-Mar5
## | GOEGSOURCENAME: Entrez Gene
## | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
## | KEGGSOURCENAME: KEGG GENOME
## | KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
## | KEGGSOURCEDATE: 2011-Mar15
## | GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)
## | GPSOURCEURL: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19
## | GPSOURCEDATE: 2010-Mar22
## | ENSOURCEDATE: 2013-Jan16
## | ENSOURCENAME: Ensembl
## | ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
## | UPSOURCENAME: Uniprot
## | UPSOURCEURL: http://www.UniProt.org/
## | UPSOURCEDATE: Thu Mar  7 17:01:43 2013


# bimap from hgu133a probe id to ENTREZID
biocann_object('ENTREZID', 'hgu133a.db')

## ENTREZID map for chip hgu133a (object of class "ProbeAnnDbBimap")


# reversed bimap from UNIGENE to hgu133a probe id
biocann_object('hgu133a.db', 'UNIGENE')

## revmap(UNIGENE) map for chip hgu133a (object of class "ProbeAnnDbBimap")

# this is equivalent to using the annotation package object (no quotes),
# when the package is already loaded (=> helpful in interactive session with auto-completion)
biocann_object(hgu133a.db, 'UNIGENE')