Walkthrough R · Data Science in Omics Introduction

Basic Workflow

The R environment is broken up into two main windows, the console and the script. The console window is the place where R is waiting for you to tell it what to do, and where it will show the results of a command. > mark that R is ready to take a command. + means the command is not complete, like you are missing a ) or }. You can type commands directly into the console, but they will be forgotten when you close the session.The script is a simple text (.R) file that stores your code. The point of a well constructed script is not just to “do stuff” but to do it in a way that maintains a complete record of your work so anyone can easily and exactly replicate your workflow and results.

Basic Operation

# this is a comment in R
Use x <- 3 to assign a value, 3, to a variable, x
- = can also be used, but should be avoided EXCEPT in functions
R counts from 1, unlike many other programming languages (e.g., Python)
length(thing) returns the number of elements contained in the variable thing. dim(thing) returns length in multiple dimensions.
c(value1, value2, value3) creates a vector
container[i] selects the i’th element from the vector container
container[[i]] selects the i’th object from the object container
You’ll have to get familiar with the different class() of objects:
- character is text
- numeric is numbers
- factor is categories
- logical is TRUE / FALSE
Objects can be grouped in many ways:
- list()
- vector() or c()
- matrix()
- data.frame()

Control Flow

Create a conditional using if, else if, and else

  if(x > 0){
      print("value is positive")
  } else if (x < 0){
      print("value is negative")
  } else{
      print("value is neither positive nor negative")
  }

Create a for loop to process elements in a collection one at a time
```
  for (i in 1:5) {
      print(i)
  }
```

This will print:

Use == to test for equality
- 3 == 3, will return TRUE,
- 'apple' == 'orange' will return FALSE
X & Y is TRUE is both X and Y are true
X | Y is TRUE if either X or Y, or both are true

Functions

Defining a function:

  is_positive <- function(integer_value){
      if(integer_value > 0){
         TRUE
      else{
         FALSE
      {
  }

In R, the last executed line of a function is automatically returned, otherwise use return() to be sure you know what the function is giving back to you.

Specifying a default value for a function argument

  increment_me <- function(value_to_increment, value_to_increment_by = 1){
      value_to_increment + value_to_increment_by
  }

increment_me(4), will return 5

increment_me(4, 6), will return 10

Call a function by using function_name(function_arguments)
apply family of functions: apply(), sapply(), lapply(), mapply() apply(dat, MARGIN = 2, mean) will return the average (mean) of each column in dat

Packages

Install package by using install.packages("package-name")
Update packages by using update.packages("package-name")
Load packages by using library("package-name")

Math

Do math by simply typing or pasting in the console.

x+y
x*y
x**y
sum(vector)
mean(vector)
round(vector, decimal_places)

Scientific Commands

Import data using read.csv(file, header = TRUE, sep = ",", …)
Check out what you imported with names(), head(), and str()
Export results using write.csv(x, file, …)
Many statistical functions are available (t.test(), lm(y~x))

Finding Help

Don’t be defeated by a coding problem, semantics confusion, or error messages. Find help:

help(function) or ?function - Input any function into the parentheses for useful syntax and function information. args() gives you the arguments of a function.

You can also check out the resources below or run a general engine search (i.e., r split character string). The hardest part here is finding the right keywords to use.

General Resources

Manual Directories

R Community Forums

How to ask for help

###Style Guides

This document benefited greatly by the inclusion of Data Carpentry materials (Before we start, Introduction to R) and Software Carpentry’s (Programming with R Reference)