Introduction to Statistics
Joao Lourenço (joao.lourenco@sib.swiss) and Rachel Marcone (rachel.marcone@sib.swiss)
January 2024
Data analysis with R:
An introduction
Data analysis workflow
Hadley Wickham
Garrett Grolemund
Prepare: make data available in a specific format
• Database
• Flat file
• Proprietary file
Which tool to use for data analysis ?
Annoyances with spreadsheets
Microsoft Excel
•Many standard methods in statistics are not available. Other
methods only offer basic options (linear regression)
• Different analysis require user to reorganize the data
•Probably ok for simple calculations (basic summary statistics,
simple regression)
•Add-ons can be used for missing functions (e.g. StatPlus for
Excel)
Libreoffice
• Many types of graphics violate standards of good graphics
Annoyances with spreadsheets
“The date conversions affect at least 30 gene names; the floating-point
conversions affect at least 2,000 if Riken identifiers are included. These
conversions are irreversible; the original gene names cannot be recovered.”
Example of a dataset which is difficult to use with any statistical program
https://en.wikipedia.org/wiki/Comparison_of_statistical_packages
What is R ?
• R is an open source complete and flexible software environment for
statistical computing and graphics.
• It includes :
• Tools for data import and manipulation
• Large set of data analysis tools
• Graphical tools
• As a programming language, a simple development environment, with a text
editor
• R itself is written primarily in C and Fortran, and is an implementation
of the statistical language S
Why R ?
• R has become the tool of choice for statistical analysis in several
fields, including life sciences
• Two reasons for this success: it is free and many contributed packages
are available (can be installed and run directly from R).
• Well-designed publication-quality plots can be produced, including
mathematical symbols and formulae where needed.
• Many tools implemented for bioinformatics
Advantages of R
• Advantages of R
▪ Availability and compatibility
▪ State-of-the-art graphics capabilities
▪ Can import files from other (statistical) programs
▪ New version every x months
▪ Interactive development environments (IDEs) available
▪ Large users community
• Advantages of learning R
▪ Learn to program and do reproducible research
▪ Speak the common language
Drawbacks of R
• «Expert friendly»
• Learn by example
• Not very (easily) interactive
• Command-based
• Documentation sometimes cryptic
• (Too) large amount of resources
• Constantly evolving
• Memory intensive and slow at times
Downloading and installing R: the R website
https://www.r-project.org/
R console
The prompt “>”
indicates that R is
waiting for you to
type a command
RStudio interface
Editor Workspace,
history
File explorer,
plots,
packages,
Console,
help
terminal
R scripts and workspace
• R script (.R file)
▪ Very useful instead of typing commands on the console.
▪ Allows you to keep track of what you are doing and make any modification easier
▪ To actually execute some commands, you can select the lines and run the execution
• Workspace (.Rdata file)
▪ The internal memory where R will store the objects you created during the session.
▪ To list what is in your workspace: ls()
▪ To empty the workspace from all objects: rm(list=ls())
▪ To save only specific R objects: save(object_name(s),"name_of_file.RData")
▪ To save your entire workspace: save.image("name_of_file.RData")
▪ To load your workspace / specific R objects: load("name_of_file.RData")
R Markdown
• R Markdown provides an authoring framework for data science. You can use a single R Markdown file to
both:
▪ save and execute code
▪ generate high quality reports that can be shared with an audience
• R Markdown documents are fully reproducible and support dozens of static and dynamic output formats
https://rmarkdown.rstudio.com/lesson-1.html
LeavingR
• Toleave R, use the q()command (or "quit" from the menu in RStudio):
> q()
Save workspace image? [y/n/c]:
Answers:
y save workspace image
n don't save workspace image
c cancel quitting
Functions, operators and variables
CIhigh <- mean(x) + 1.96*sd(x)/sqrt(n)
Variables: objects stored in memory
Functions: always followed by parenthesis
Operators
R syntax
• Case sensitive: A is not a
• Variable names can include A-Z, a-z, 0-9, .… but can not start with a
number
• Commands can be separated by ; or newline
> x <- 2; x+2
[1] 4
• # indicates comments:
> maxvalue <- 2 # Data above two is not relevant
R help
> ?sum # equivalent to help(sum)
Using R as a calculator
> 2*3
[1] 6
>log(6)/2^2
[1] 0.4479399
>exp(6)-4
[1] 399.4288
> pi-3
[1] 0.1415927
Using R as a programming language
> x <- 2.0
> x
[1] 2.0
> y = 3.0 # Equivalent to y <- 3.0
> y; x
[1] 3
[1] 2
>1/x
[1] 0.5
Creating vectors using the c() command
> x <- c(1.3, 0.32 10.5, 5.9, 6.3)
,
> x
[1] 1.30 0.32 10.5 5.90 6.30
0
> y <- c(x, 1.4, x, x); y
[1] 1.30 0.32 10.5 5.90 6.30
0
[6] 1.40 1.30 0.32 10.50 5.90
[11] 6.30 1.30 0.3 10.50 5.90
2
[16] 6.30
Vector operations
Vector operations work element by element:
> x <- c(1.3, 0.32, 10.5, 5.9, 6.3)
> y <- x*2; y
[1] 2.60 0.64 21.00 11.80 12.60
>z <- x*y; z
[1] 3.38 0.21 220.50 69.62 79.38
Recycling
• If a vector is too short, R recycles it (reuses it) as needed:
> x <- c(1.3, 0.32, 10.5, 5.9)
> y <- c(2, 10)
> x*y
[1] 2.6 3.2 21.0 59.0
1.3*2 0.32*10 10.5*2 5.9*10
• A warning message is displayed if the shortest vector can not be recycled entirely:
> x <- c(1.3, 0.32, 10.5, 5.9, 6.3)
> x*y
[1] 2.6 3.2 21.0 59.0 12.6
Warning message:
In x * y :
longer object length is not a multiple of shorter object length
Generating sequences of numbers
> 1:10
[1] 1 2 3 4 5 6 7 8 9 10
This is equivalent to:
>c(1,2,3,4,5,6,7,8,9,10)
[1] 1 2 3 4 5 6 7 8 9 10
> 10:1
[1] 10 9 8 7 6 5 4 3 2 1
Beware of operator priority
> x <- 2*1:10
# equivalent to x <- 2*(1:10)
> x
[1] 2 4 6 8 10 12 14 16 18 20
> n <- 10
> 1:n-1
# equivalent to (1:n)-1
[1] 0 1 2 3 4 5 6 7 8 9
> 1:(n-1)
[1] 1 2 3 4 5 6 7 8 9
The seq() function: the same, but more flexible
> seq(from=1, to=10)
[1] 1 2 3 4 5 6 7 8 9 10
> seq(from=1, to=5, by=0.5)
[1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0
> x <- seq(from=1, to=5, length=17)
> x
[1] 1.00 1.25 1.50 1.75 2.00 2.25 2.50 2.75
[9] 3.00 3.25 3.50 3.75 4.00 4.25 4.50 4.75
[17 5.0
] 0
Non numeric vectors: boolean (logical) values
> x <- seq(from=1, to=5, length=17)
> x
[1] 1.00 1.25 1.50 1.75 2.00 2.25 2.50 2.75
[9] 3.00 3.25 3.50 3.75 4.00 4.25 4.50 4.75
[17] 5.00
> y <- x<5 # help(“<”) shows list of relational operators
> y
[1] TRUE TRUE TRUE TRUE TRUE TRUE
[7] TRUE TRUE TRUE TRUE TRUE TRUE
[13] TRUE TRUE FALSE
>sum(x<5)
[1] 16
Missing values are designated by NA
> z <- c(1:3,NA)
> z
[1] 1 2 3 NA
> is.na(z)
[1] FALSE FALSE FALSE TRUE
> mean(z)
[1] NA
> mean(z, na.rm=TRUE)
[1] 2
Character strings
> char <- c("hello","world","!"); char
[1] "hello" "world" "!"
Vectors can not combine numbers and characters:
> char <- c("hello",3:5,"world"); char
[1] "hello" "3" "4" "5" "world"
> char <- c(char, NA); char
[1] "hello" "3" "4" "5" "world" NA
Selecting subsets of vectors using [ ]
> x <- 10:30
> x[2]
[1] 11
> x[1:5]
[1] 10 11 12 13 14
Selecting subsets of vectors using [ ] and boolean vectors
> x <- 10:30
> x[x>25]
[1] 26 27 28 29 30
>x <-c(seq(from=5, to=10,by=0.5),NA,
seq(from=11,to=15,by=0.5),NA,
seq(from=16,to=20,by=0.5))
> x[!is.na(x)]
[1] 5.0 5.5 6.0 6.5 7.0 7.5 8.0 8.5
[9] 9.0 9.5 10.0 11.0 11.5 12.0 12.5 13.0
[17] 13.5 14.0 14.5 15.0 16.0 16.5 17.0 17.5
[25] 18.0 18.5 19.0 19.5 20.0
Changing parts of vectors using [ ]
> x[32] <- 200
> x[c(10,29)] <- c(1,100)
> x[x>15] <- NA
Finding the length of a vector
> x <- 1:5
> length(x)
[1] 5
> y <- 1:16
>len <- length(y) ; len
[1] 16
Data analysis workflow
Importing data into R
• R can import flat files using e.g. the commands:
read.table()
read.csv()
read.delim()
(with many options – check the help).
• R can also:
▪ Read Excel spreadsheets
▪ Read plenty of other formats
▪ Directly access databases
▪ Access files over the web
Data frames
• Data frames are made of columns having all the same number of elements
• They look like matrices, except that the columns can hold different variables
types
• They are typically used to store data, with
▪ Each row being an experimental unit
▪ Each column being a measurement
> data[,1] # access first column
> data[, "data1"] # access column "data1"
> data$data1 # … same
Creating data frames
> x <- 1:10
> y <- seq(from=5,to=10,length=10)
> z <- c("A","B","B","A","A","A","B","A","B","B")
> df <- data.frame(d1=x, d2=y, fact=z)
> df
d1 d2 fact
1 1 5.000000 A
2 2 5.555556 B
..
> names(df)
[1] "d1" "d2" "fact“
>dim(df)
[1] 10 3
Adding new columns
> df$d3 <- 10:1
> df
d1 d2 fact d3
1 1 5.000000 A 10
2 2 5.555556 B 9
…
> summary(df)
d1 d2 fact d3
Min. : 1.00 Min. : 5.00 Length:10 Min. : 1.00
1st Qu.: 3.25 1st Qu.: 6.25 Class :character 1st Qu.: 3.25
Median : 5.50 Median : 7.50 Mode :character Median : 5.50
Mean : 5.50 Mean : 7.50 Mean : 5.50
3rd Qu.: 7.75 3rd Qu.: 8.75 3rd Qu.: 7.75
Max. :10.00 Max. :10.00 Max. :10.00
Select data from a data frame
• Select all valuesof "d2" for which "fact" is "B"
> df[ df$fact == "B", "d2" ]
[1] 5.555556 6.111111 8.333333 9.444444 10.000000
• Select all values of "d1" for which "fact"is "B " and "d2" > 7
> df[ (df$fact == "B" & df$d2 > 7), "d1" ]
[1] 7 9 10
• Select all values of "d3" for which "fact" is “A " or "d2" < 6
>df[ (df$fact == "B" | df$d2 < 6), "d3" ]
[1] 10 9 8 4 2 1
Exercise
• Import students.csv into a variable (call it data)
• Extract the weight of women only in a new
variable
• Extract the weights of the people who weight
more than 80 kilos
• Extract the entries of men who weight more
than 80 kg (you can use the "&" operator to
include two conditions)
If you do not know what to do:
1.Extract the weight of women only in
a new variable
2.Extract the weights of the people
who weight more than 80 kilos
3.Extract the entries of men who
weight more than 80 kg
[you can use the "&" operator to
include two conditions]
