Covers: Chapter 16 - R code

R Code Style and Best Practices

Formatting (hard rules)

• Use <- for assignment; = only for named function arguments.
• Indent with 4 spaces. No tabs.
• No lines longer than 80 characters.
• Space around binary operators: a == b. No space around = in named arguments: somefunc(a=1, b=2).
• Full-line comments start with ##, indented to surrounding code.

Naming

• Functions and variables: camelCase starting lowercase (myFunction).
• Classes: CamelCase starting uppercase (MyClass).
• Do NOT put . in function names (avoids S3 dispatch collisions).
• Prefix non-exported/internal functions with a dot: .internalFunc.

Vectorization and iteration

• Write seq_len(n) or seq_along(x), NOT 1:n or 1:length(x) (the latter break when length is 0).
• Prefer vectorized code over explicit for loops.
• Use vapply() instead of sapply() (type-safe).
• Pre-allocate and fill (via lapply()/vapply()); never copy-and-append in a loop (that is O(n^2)).

Booleans

• Use TRUE/FALSE, never T/F.

Functions

• Write small functions; avoid functions longer than one screen.
• Give arguments defaults where sensible; validate with stopifnot() or checks.

Forbidden patterns

• set.seed() inside package/internal code.
• browser() left in code.
• Direct slot access with @ or slot() - use accessor methods instead.
• <<- (superassignment).
• system() without justification - use system2().
• Nested function definitions.
• Commented-out code blocks and TODO comments in published packages.

Messaging

• message() for diagnostic messages.
• warning() for unusual-but-handled situations.
• stop() for errors.
• cat()/print() only inside show() methods, not for general messaging.

Classes and methods

• Prefer S4 over S3. Provide constructor functions and show() methods.
• Use accessors, not direct slot access.
• Only define methods for classes exported by your own package.
• Reuse existing Bioconductor core classes rather than inventing new ones.

Web access, caching, parallelism

• Never write to the user home, working, or installed-package directory.
• Cache downloads via BiocFileCache or tools::R_user_dir(package, which="cache"); use tempfile() for scratch.
• Parallel operations should default to 1 or 2 cores.

Source: R code Fetched 2026-08-14 from contributions.bioconductor.org (Bioconductor devel guide).