[BioC] learning Bioconductor - some help for newbies

[Naomi Altman]

Speaking as someone who uses Bioconductor due to its extensibility, I 
cannot agree with the statement posted a couple of weeks ago to the list:

"You should not really need to know about the classes -> they should
   be relatively transparent at the user level. "

In order to do anything not written into Bioconductor, I needed to 
understand the classes.  The documentation is good - once I understood what 
it meant.  So, to help others, here are some things I learned.

Every object in R has a class.  However, some classes are more elementary 
(e.g. vectors, matrices, tables) and elements are extracted by giving the 
index (e.g. v[3], or m[1,4]).   Many R functions return objects which are 
lists. Components of a list can be extracted by name (list$mydata) or by 
component number (list[[3]]).  Anything you extract also has a class.

Most Bioconductor objects are NOT elementary.  The data stored in the 
Bioconductor objects are extracted by functions which are listed in the 
documentation.   These are called slots.  e.g. maRf(myRawMarray)   extracts 
the red foreground from an marrayRaw object).  (The ?marrayRaw file was 
extremely helpful in helping me understand all of this.)


Here are some important commands to know:

class(myobject)           prints the class of your object
?objectclass                prints the documentation for the class 
"objectclass"

names(mylist)             prints the names of the elements of a list
attributes(myobject)     gives more information about the object
methods(myobject)      prints the methods associated with myobject

function.class              (e.g. plot.ProbeSet is the function that is 
actually called if you type plot(myprobeset) )

--Naomi


Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111