affycoretools (version 1.38.0)

annBM: Select Available Annotation from a Biomart

Description

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.

Usage

annBM(mart, annot, species)

Arguments

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.

species

A species name, of the form e.g., 'hsapiens'

Value

Normally called by an end user to output a character vector of annotation sources.

Details

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.

Examples

annBM()