Welcome to the course

Joining Data with data.table in R

Scott Ritchie

Postdoctoral Researcher in Systems Genomics

Joining data.tables

Combine information from two data.tables into a single data.table

Course overview

Chapter 1: Joining data with merge()
Chapter 2: Joins in the data.table workflow
Chapter 3: Troubleshooting joins
Chapter 4: Concatenating and reshaping data.tables

Table keys

Columns that link information across two tables

library(data.table)

demographics <- data.table(name   = c("Trey", "Matthew", "Angela"), 
                           gender = c(NA, "M", "F"), 
                           age    = c(54, 43, 39))

shipping <- data.table(name    = c("Matthew", "Trey", "Angela"), 
                       address = c("7 Mill road", "12 High street", 
                                   "33 Pacific boulevard"))

Inspecting `data.tables` in your R session

The tables() function will show you all data.tables loaded in your R session

tables()

           NAME NROW NCOL MB            COLS KEY
1: demographics    3    3  0 name,gender,age    
2:     shipping    3    2  0    name,address    
Total: 0MB

Inspecting `data.tables` in your R session

The str() will show you the type of each column in a single data.table

str(demographics)

Classes ‘data.table’ and 'data.frame':    3 obs. of  3 variables:
 $ name  : chr  "Trey" "Matthew" "Angela"
 $ gender: chr  NA "M" "F"
 $ age   : num  54 43 39
 - attr(*, ".internal.selfref")=<externalptr>

Inspecting `data.tables` in your R session

demographics_all

         name sex age
  1:     Trey  NA  54
  2:  Matthew   M  43
  3:   Angela   F  39
  4: Michelle   F  63
  5:  Mohamed   M  26
 ---                 
102:  Patrick   M  27
103:      Wei   F  41
104:     Adam   M  33
105:  Somchai   M  53
106:     Alma   F  19

Let's practice!

Joining Data with data.table in R