annBM {affycoretools} | R Documentation |
These functions are designed to do two things that are useful for an end
user. If called with no arguments, they will output a character vector
of annotation sources that are typically available from a Biomart
database. If called with a 'mart' connection (typically created by a
call to useMart
), they will return a character
vector of annotation sources that exist for that particular Biomart
and species. If called with a 'mart' connection and a character vector
of annotation sources, they will return a list that is intended to be
used by other functions for creating HTML pages. This last function
doesn't have any real utility for the end user.
annBM(mart, annot) linksBM(mart, annot, affyid = FALSE, ann.source = NULL)
mart |
A 'mart' connection, typically created by a
call to useMart . |
annot |
A character vector of annotation sources. This is not typically useful for an end user to specify. |
affyid |
Boolean. Are the IDs being annotated Affymetrix IDs? |
ann.source |
Character. The filter name to use if we are annotating Affymetrix IDs. |
The purpose of these functions is to either give an example of typical annotation sources that may be available at a particular Biomart, or to output those sources that are known to exist at a Biomart.
linksBM
is intended to list those annotation sources that may
be turned into hyperlinks whereas annBM
is intended to list
those annotation sources that will not be linked.
These functions have only a few of the possible annotation sources, and currently there is no simple way to extend these sources. Additions to the list are possible, however. Please contact me if there is something in particular that should be included in either list.
Normally called by an end user to output a character vector of annotation sources.
James W. MacDonald <jmacdon@med.umich.edu>
annBM()