README.Rmd

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output: md_document
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# Object-oriented programming in R

Object-oriented programming (OOP) can help us encapsulate complex data structures into a simple interface. 

## OOP concepts

- Encapsulation - related data is stored and handled together
- Polymorphism - the most appropriate function is called based on the object type (e.g various plot functions)
- Inheritance - code reuse by hierarchy of more-to-less general object types

In R, everything has a class (i.e type):

```{r}
class("Hello")
class(1:5)
class(2.1)
class(table(c(1,4,5,3,2,1)))
class(plot)
x = 10
class(x)
```

# OOP in R

Unlike other main-stream languages, R has multiple OOP systems that co-exist in parallel:

- S3 - used in base R
- S4 - _de-facto_ standard in Bioconductor
- Reference classes (RC) - used in special use cases

S3 and S4 are similar, but S4 is more formal. RC is quite different and is Java-like. 

# Sections

- [S3 OOP](s3.md)
- [S4 OOP](s4.md)
- [RC OOP](rc.md)