creating a database

Can a simple matrix be used for this or would it be better and more 
efficient to create an external database to hold the data.  If so, 
should the database be created using C and how would I do this (seeing 
as that I have never programmed in C)?

You don't want to be down at the C level, most likely:  it would be much 
more straightforward and programmer-efficient to use one of the available 
bindings to one of the available open-source databases.

R has useful / usable bindings to postgresql, sqlite, and mysql, among 
many others.

These are, however, more generally useful when you reach the point that 
you simply can't manage the volume of your data in R objects or in data 
frames. [And, well, you can go a LONG way with intelligently named R 
objects.  :-)]

--elijah