As a user it can be useful to recognize S4 objects and to learn some facts about how to explore, manipulate and use the help system when encountering S4 classes and methods.

[hr]Important note for programmers
If you have experience with object oriented programming in other languages, for example java, you need to understand that in R, S4 objects and methods are completely separate. You can use S4 classes without every using S4 methods and vice versa.

S3 and S4 classes

Based on years of experience in Bioconductor, it is fair to say that S4 classes have been very successful in this project. S4 classes has allowed us to construct rich and complicated data representations that nevertheless seems simple to the end user. An example, which we will return to, are the data containers ExpressionSet and SummarizedExperiment.

Let us look at a S3 object, the output of the linear model function lm in base R:

In standard R, an S3 object is essentially a list with a class attribute on it. The problem with S3 is that we can assign any class to any list, which is nonsense. Let us try an example

At least we don’t get an error when we print it.

S4 classes have a formal definition and formal validity checking. To the end user, this gurantees validity of the object.

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R has three object oriented (OO) systems: [[S3]], [[S4]] and [[R5]]. This page describes S4.

Compared to S3, the S4 object system is much stricter, and much closer to other OO systems. I recommend you familiarise yourself with the way that [[S3]] works before reading this document - many of underlying ideas are the same, but the implementation is much stricter. There are two major differences from S3:

formal class definitions: unlike S3, S4 formally defines the representation and inheritance for each class

multiple dispatch: the generic function can be dispatched to a method based on the class of any number of argument, not just one

Here we introduce the basics of S4, trying to stay away from the esoterica and focussing on the ideas that you need to understand and write the majority of S4 code.

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S4 Classes and Methods

y ~ normal(x * beta, sigma);

there is no longer an intercept coefficient alpha. Instead, we have assumed that the first column of the input matrix x is a column of 1 values. This way, beta[1] plays the role of the intercept. If the intercept gets a different prior than the slope terms, then it would be clearer to break it out. It is also slightly more efficient in its explicit form with the intercept variable singled out because there’s one fewer multiplications; it should not make that much of a difference to speed, though, so the choice should be based on clarity.

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