CellMix 1.6

Retrieving ID Conversion Maps

Description

Computes a complete list of maps to apply in order to convert from one type of gene identifier to another.

Usage

biocann_map(from, to, keys = NULL, cache = TRUE, link = "ENTREZID", lib = NULL, verbose = FALSE)

Arguments

from
the source tyep of gene identifier specified as a GeneIdentifierType-class object, or a character string, e.g. 'ENTREZID', if to already contains annotation data.
to
the source tyep of gene identifier specified as a GeneIdentifierType-class object, or a character string, e.g. 'UNIGENE', if from already contains annotation data.
keys
character vector of gene identifiers to map. This is only used when performing cross-species mapping.
cache
logical that indicates if -- lengthy -- cross-species mappings should be cached, so that subsequent calls with the same set of keys returns much faster.
link
the gene identifier type to use to link between platforms. We strongly recommend to leave this argument as default 'ENTREZID'.
lib
path to the library (ie. directory) where to first look and install any required annotation packages. This library is temporarly prepended to the .libPath, so that user and R standard library locations are still looked up.
verbose
logical or integer that indicates the level of verbosity.

Details

This function is an extension/enhancement of the function GSEABase:::.mapIdentifiers_selectMaps, which cope with the cases of cross-platform and cross-species conversions.

In particular, when called in an interactive session, this function will notifies the user about missing required annotation packages, and offers to install them at runtime.

Examples


## Not run: 
##D # intra-platform
##D m <- biocann_map('ENTREZID', AnnotationIdentifier('hgu133a.db'))
##D # cross platform
##D m <- biocann_map(UnigeneIdentifier('hgu133a.db'), EntrezIdentifier('hgu133b.db'))
##D # cross platform, cross-species
##D m <- biocann_map(EntrezIdentifier('hgu133a.db')
##D                     , AnnotationIdentifier('mogene10stprobeset.db')
##D                     , keys=as.character(1:1000))
## End(Not run)