R – a brief

introduction
Original material

 Johannes Freudenberg
 Cincinnati Children’s Hospital Medical Center
 Marcel Baumgartner
 Nestec S.A.
 Jaeyong Lee
 Penn State University
 Jennifer Urbano Blackford, Ph.D
 Department of Psychiatry, Kennedy Center
 Wolfgang Huber
History of R

 Statistical programming language S developed at

Bell Labs since 1976 (at the same time as UNIX)
 Intended to interactively support research and
data analysis projects
 Exclusively licensed to Insightful (“S-Plus”)
 R: Open source platform similar to S developed
by R. Gentleman and R. Ihaka (U of Auckland, NZ)
during the 1990s
 Since 1997: international “R-core” developing
team
 Updated versions available every couple months
What R is and what it is not

 R is
 a programming language
 a statistical package
 an interpreter
 Open Source
 R is not
 a database
 a collection of “black boxes”
 a spreadsheet software package
 commercially supported
What R is

 data handling and storage: numeric, textual

 matrix algebra
 hash tables and regular expressions
 high-level data analytic and statistical functions
 classes (“OO”)
 graphics
 programming language: loops, branching,
subroutines
What R is not

 is not a database, but connects to DBMSs

 has no click-point user interfaces, but connects to
Java, TclTk
 language interpreter can be very slow, but allows
to call own C/C++ code
 no spreadsheet view of data, but connects to
Excel/MsOffice
 no professional /commercial support
R and statistics

 Packaging: a crucial infrastructure to efficiently

produce, load and keep consistent software
libraries from (many) different sources / authors

 Statistics: most packages deal with statistics and

data analysis

 State of the art: many statistical researchers

provide their methods as R packages
Getting started

 To obtain and install R on your computer

 Go to [Link] to choose a
mirror near you
 Click on your favorite operating system (Linux, Mac, or
Windows)
 Download and install the “base”
 To install additional packages
 Start R on your computer
 Choose the appropriate item from the “Packages” menu
R: session management

 Your R objects are stored in a workspace

 To list the objects in your workspace: > ls()
 To remove objects you no longer need:
> rm(weight, height, bmi)
 To remove ALL objects in your workspace:
> rm(list=ls()) or use Remove all objects in the
Misc menu
 To save your workspace to a file, you may type
> [Link]() or use Save Workspace… in the
File menu
 The default workspace file is called .RData
Basic data types
Objects

 names
 types of objects: vector, factor, array, matrix,
[Link], ts, list
 attributes
 mode: numeric, character, complex, logical
 length: number of elements in object
 creation
 assign a value
 create a blank object
Naming Convention

 must start with a letter (A-Z or a-z)

 can contain letters, digits (0-9), and/or periods “.”

 case-sensitive
 mydata different from MyData

 do not use use underscore “_”

Assignment

 “<-” used to indicate assignment

x<-c(1,2,3,4,5,6,7)
x<-c(1:7)
x<-1:4

 note: as of version 1.4 “=“ is also a valid assignment

operator
R as a calculator

> 5 + (6 + 7) * pi^2
[1] 133.3049
> log(exp(1))
[1] 1
> log(1000, 10)
[1] 3
> sin(pi/3)^2 + cos(pi/3)^2
[1] 1
> Sin(pi/3)^2 + cos(pi/3)^2
Error: couldn't find function "Sin"
 R as a calculator

1.0
> log2(32)
[1] 5

0.5
sin(seq(0, 2 * pi, length = 100))
> sqrt(2)

0.0
[1] 1.414214

-0.5
> seq(0, 5, length=6)
[1] 0 1 2 3 4 5 -1.0

0 20 40 60 80 100

Index

> plot(sin(seq(0, 2*pi, length=100)))

Basic (atomic) data types

 Logical  Character
> x <- T; y <- F > a <- "1"; b <- 1
> x; y > a; b
[1] TRUE [1] "1"
[1] 1
[1] FALSE
> a <- "character"
 Numerical
> b <- "a"; c <- a
> a <- 5; b <- sqrt(2) > a; b; c
> a; b [1] "character"
[1] 5 [1] "a"
[1] 1.414214 [1] "character"
Vectors, Matrices, Arrays

 Vector
 Ordered collection of data of the same data type
 Example:
 last names of all students in this class

 Mean intensities of all genes on an oligonucleotide

microarray
 In R, single number is a vector of length 1
 Matrix
 Rectangular table of data of the same type
 Example
 Mean intensities of all genes measured during a microarray

experiment
 Array
 Higher dimensional matrix
Vectors

 Vector: Ordered collection of data of the same

data type
> x <- c(5.2, 1.7, 6.3)
> log(x)
[1] 1.6486586 0.5306283 1.8405496
> y <- 1:5
> z <- seq(1, 1.4, by = 0.1)
>y+z
[1] 2.0 3.1 4.2 5.3 6.4
> length(y)
[1] 5
> mean(y + z)
[1] 4.2
 Vecteurs

> Mydata <- c(2,3.5,-0.2) Vector (c=“concatenate”)

> Colors <-
c("Red","Green","Red") Character vector

> x1 <- 25:30

> x1
[1] 25 26 27 28 29 30 Number sequences

> Colors[2]
[1] "Green" One element

> x1[3:5]
[1] 27 28 29 Various elements
Operation on vector elements

> Mydata
[1] 2 3.5 -0.2

> Mydata > 0  Test on the elements

[1] TRUE TRUE FALSE

> Mydata[Mydata>0]  Extract the positive

[1] 2 3.5 elements

> Mydata[-c(1,3)]
[1] 3.5  Remove elements
 Vector operations
> x <- c(5,-2,3,-7)
> y <- c(1,2,3,4)*10 Operation on all the elements
>y
[1] 10 20 30 40

> sort(x) Sorting a vector

[1] -7 -2 3 5

> order(x)
[1] 4 2 3 1 Element order for sorting

> y[order(x)]
[1] 40 20 30 10 Operation on all the components

> rev(x) Reverse a vector

[1] -7 3 -2 5
Matrices
 Matrix: Rectangular table of data of the same type
> m <- matrix(1:12, 4, byrow = T); m
[,1] [,2] [,3]
[1,] 1 2 3
[2,] 4 5 6
[3,] 7 8 9
[4,] 10 11 12
> y <- -1:2
> [Link] <- m + y
> t([Link])
[,1] [,2] [,3] [,4]
[1,] 0 4 8 12
[2,] 1 5 9 13
[3,] 2 6 10 14
> dim(m)
[1] 4 3
> dim(t([Link]))
[1] 3 4
 Matrices
Matrix: Rectangular table of data of the same type

> x <- c(3,-1,2,0,-3,6)

> [Link] <- matrix(x,ncol=2) Matrix with 2 cols
> [Link]
[,1] [,2]
[1,] 3 0
[2,] -1 -3
[3,] 2 6

> [Link] <- matrix(x,ncol=2,

byrow=T) By row creation
> [Link]
[,1] [,2]
[1,] 3 -1
[2,] 2 0
[3,] -3 6
Dealing with matrices

> [Link][,2] 2nd col

[1] -1 0 6

> [Link][c(1,3),] 1st and 3rd lines

[,1] [,2]
[1,] 3 -1
[2,] -3 6

> [Link][-2,] No 2nd line

[,1] [,2]
[1,] 3 -1
[2,] -3 6
 Dealing with matrices
> dim([Link]) Dimension
[1] 3 2
> t([Link]) Transpose
[,1] [,2] [,3]
[1,] 3 2 -3
[2,] -1 0 6

> [Link] %*% t([Link]) Multiplication

[,1] [,2] [,3]

[1,] 10 6 -15
[2,] 6 4 -6
[3,] -15 -6 45

> solve() Inverse of a square matrix

> eigen() Eigenvectors and eigenvalues
Missing values

 R is designed to handle statistical data and

therefore predestined to deal with missing values
 Numbers that are “not available”
> x <- c(1, 2, 3, NA)
>x+3
[1] 4 5 6 NA
 “Not a number”
> log(c(0, 1, 2))
[1] -Inf 0.0000000 0.6931472
> 0/0
[1] NaN
 Subsetting

 It is often necessary to extract a subset of a

vector or matrix
 R offers a couple of neat ways to do that
> x <- c("a", "b", "c", "d", "e", "f", "g", "h")
> x[1]
> x[3:5]
> x[-(3:5)]
> x[c(T, F, T, F, T, F, T, F)]
> x[x <= "d"]
> m[,2]
> m[3,]
Lists, data frames,
and factors
Lists
vector: an ordered collection of data of the same
type.
> a = c(7,5,1)
> a[2]
[1] 5

list: an ordered collection of data of arbitrary types.

> doe = list(name="john",age=28,married=F)
> doe$name
[1] "john“
> doe$age
[1] 28

Typically, vector elements are accessed by their

index (an integer), list elements by their name (a
Lists 1

 A list is an object consisting of objects called

components.
 The components of a list don’t need to be of the
same mode or type and they can be a numeric
vector, a logical value and a function and so on.
 A component of a list can be referred as aa[[I]] or
aa$times, where aa is the name of the list and
times is a name of a component of aa.
Lists 2

 The names of components may be abbreviated

down to the minimum number of letters needed
to identify them uniquely.
 aa[[1]] is the first component of aa, while aa[1] is
the sublist consisting of the first component of aa
only.
 There are functions whose return value is a List.
We have seen some of them, eigen, svd, …
Lists are very flexible
> [Link] <- list(c(5,4,-1),c("X1","X2","X3"))
> [Link]
[[1]]:
[1] 5 4 -1

[[2]]:
[1] "X1" "X2" "X3"

> [Link][[1]]
[1] 5 4 -1

> [Link] <- list(c1=c(5,4,-1),c2=c("X1","X2","X3"))

> [Link]$c2[2:3]
[1] "X2" "X3"
Lists: Session

Empl <- list(employee=“Anna”, spouse=“Fred”, children=3,

[Link]=c(4,7,9))
Empl[[4]]
Empl$child.a
Empl[4] # a sublist consisting of the 4th component of Empl
names(Empl) <- letters[1:4]
Empl <- c(Empl, service=8)
unlist(Empl) # converts it to a vector. Mixed types will be converted to
character, giving a character vector.
 More lists

> [Link]
[,1] [,2]
[1,] 3 -1
[2,] 2 0
[3,] -3 6

> dimnames([Link]) <- list(c("L1","L2","L3"),

c("R1","R2"))

> [Link]
R1 R2
L1 3 -1
L2 2 0
L3 -3 6
Data frames
data frame: represents a spreadsheet.
Rectangular table with rows and columns; data
within each column has the same type (e.g.
number, text, logical), but different columns may
have different types.
Example:
> cw = chickwts
> cw
weight feed
1 179 horsebean
11 309 linseed
23 243 soybean
37 423 sunflower
...
Data Frames 1

 A data frame is a list with class “[Link]”. There are

restrictions on lists that may be made into data frames.
 a. The components must be vectors (numeric,
character, or logical), factors, numeric matrices, lists, or
other data frames.
 b. Matrices, lists, and data frames provide as many
variables to the new data frame as they have columns,
elements, or variables, respectively.
 c. Numeric vectors and factors are included as is, and
non-numeric vectors are coerced to be factors, whose
levels are the unique values appearing in the vector.
 d. Vector structures appearing as variables of the data
frame must all have the same length, and matrix structures
must all have the same row size.
Subsetting
Individual elements of a vector, matrix, array or data frame
are accessed with “[ ]” by specifying their index, or their
name
> cw = chickwts
> cw
weight feed
1 179 horsebean
11 309 linseed
23 243 soybean
37 423 sunflower
...

> cw [3,2]
[1] horsebean
6 Levels: casein horsebean linseed ... sunflower
> cw [3,]
weight feed
3 136 horsebean
Subsetting in data frames

 an = Animals
 an

body brain
Mountain beaver 1.350 8.1
Cow 465.000 423.0
Grey wolf 36.330 119.5
> an [3,]
body brain
Grey wolf 36.33 119.5
Labels in data frames
> labels (an)
[[1]]
[1] "Mountain beaver" "Cow"
[3] "Grey wolf" "Goat"
[5] "Guinea pig" "Dipliodocus"
[7] "Asian elephant" "Donkey"
[9] "Horse" "Potar monkey"
[11] "Cat" "Giraffe"
[13] "Gorilla" "Human"
[15] "African elephant" "Triceratops"
[17] "Rhesus monkey" "Kangaroo"
[19] "Golden hamster" "Mouse"
[21] "Rabbit" "Sheep"
[23] "Jaguar" "Chimpanzee"
[25] "Rat" "Brachiosaurus"
[27] "Mole" "Pig"

[[2]]
[1] "body" "brain"
Control structures and
functions
Grouped expressions in R

x = 1:9

if (length(x) <= 10)

{
x <- c(x,10:20);
print(x)
}
else
{
print(x[1])
}
Loops in R

>for(i in 1:10) {
x[i] <- rnorm(1)
}
j=1
while( j < 10) {
print(j)
j <- j + 2
}
Functions
 Functions do things with data
 “Input”: function arguments (0,1,2,…)
 “Output”: function result (exactly one)

 Example:
add = function(a,b)
{ result = a+b
return(result) }

 Operators:
 Short-cut writing for frequently used functions of one or two
arguments.
 Examples: + - * / ! & | %%
General Form of Functions

function(arguments) {
expression
}

larger <- function(x,y) {

if(any(x < 0)) return(NA)
[Link] <- y > x
x[[Link]] <- y[[Link]]
x
}
Functions inside functions

120
100
80
dist

60
40
20
0
> attach(cars) 5 10 15

speed
20 25

> plot(speed,dist)
> x <- seq(min(speed),max(speed),length=1000)
> newdata=[Link](speed=x)))
> lines(x,predict(lm(dist~speed),newdata))

> rm(x) ; detach()

If you are in doubt...

> help (predict)

'predict' is a generic function for predictions from
the results
of various model fitting functions.
> help ([Link])
'[Link]' produces predicted values, obtained
by evaluating the
regression function in the frame 'newdata'
> predict(lm(dist~speed),newdata)
Calling Conventions for Functions

 Arguments may be specified in the same order in

which they occur in function definition, in which
case the values are supplied in order.
 Arguments may be specified as name=value, when
the order in which the arguments appear is
irrelevant.
 Above two rules can be mixed.

> [Link](x1, y1, [Link]=F, [Link]=.99)

> [Link]([Link]=F, [Link]=.99, x1, y1)
Missing Arguments

 R function can handle missing arguments two

ways:

 either by providing a default expression in the

argument list of definition, or

 by testing explicitly for missing arguments.

Missing Arguments in Functions

> add <- function(x,y=0){x + y}

> add(4)

> add <- function(x,y){

if(missing(y)) x
else x+y
}
> add(4)
Variable Number of Arguments

 The special argument name “…” in the function

definition will match any number of arguments in
the call.

 nargs() returns the number of arguments in the

current call.
Variable Number of Arguments

> [Link] <- function(…) mean(c(…))

> [Link](1:10,20:100,12:14)

> [Link] <- function(…)

{
means <- numeric()
for(x in list(…)) means <- c(means,mean(x))
mean(means)
}
Variable Number of Arguments

[Link] <- function(…)

{
n <- nargs()
means <- numeric(n)
all.x <- list(…)
for(j in 1:n) means[j] <- mean(all.x[[j]])
mean(means)
}
[Link](1:10,10:100)
Useful functions

> seq(2,12,by=2)
[1] 2 4 6 8 10 12
> seq(4,5,length=5)
[1] 4.00 4.25 4.50 4.75 5.00
> rep(4,10)
[1] 4 4 4 4 4 4 4 4 4 4

> paste("V",1:5,sep="")
[1] "V1" "V2" "V3" "V4" "V5"

> LETTERS[1:7]
[1] "A" "B" "C" "D" "E" "F" "G"
 Mathematical operation

Opérations usuelles : + - * /
Puissances: 2^5 ou bien 2**5
Divisions entières: %/%
Modulus: %% (7%%5 gives 2)

Fonctions standards: abs(), sign(), log(), log10(), sqrt(),

exp(), sin(), cos(), tan()
gamma(), lgamma(), choose()

Pour arrondir: round(x,3) arrondi à 3 chiffres après la virgule

Et aussi: floor(2.5) donne 2, ceiling(2.5) donne 3

Vector functions
> vec <- c(5,4,6,11,14,19)
> sum(vec)
[1] 59 And also: min() max()
> prod(vec) cummin() cummax()
[1] 351120 range()
> mean(vec)
[1] 9.833333
> median(vec)
[1] 8.5
> var(vec)
[1] 34.96667
> sd(vec)
[1] 5.913262
> summary(vec)
Min. 1st Qu. Median Mean 3rd Qu. Max.
4.000 5.250 8.500 9.833 13.250 19.000
Des fonctions logiques

R contient deux valeurs logiques: TRUE (ou T) et FALSE (ou F).

Exemple: == exactement égal
< plus petit
> 3 == 4 > plus grand
[1] FALSE <= plus petit ou égal
> 4 > 3 >= plus grand ou égal
[1] TRUE != différent
& “et” (“and”)
> x <- -4:3 | “ou” (“or”)
> x > 1
[1] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE
> sum(x[x>1])
[1] 5
Notez la différence !
> sum(x>1)
[1] 2
Graphics in R
Plot()

 If x and y are vectors, plot(x,y) produces a

scatterplot of x against y.
 plot(x) produces a time series plot if x is a
numeric vector or time series object.
 plot(df), plot(~ expr), plot(y ~ expr), where df is a
data frame, y is any object, expr is a list of object
names separated by `+' (e.g. a + b + c).
 The first two forms produce distributional plots of
the variables in a data frame (first form) or of a
number of named objects (second form). The
third form plots y against every object named in
expr.
 Graphics with plot()

> plot(rnorm(100),rnorm(100))

The function rnorm()

3

Simulates a random normal

distribution .
2
1
rnorm(100)

Help ?rnorm,
and ?runif,
0

?rexp,
-1

?binom, ...
-2

-3 -2 -1 0 1 2
rnorm(100)
Graphics with plot()
> x <- seq(-2*pi,2*pi,length=100)
> y <- sin(x)

> par(mfrow=c(2,2)) Une Ligne

1.0

1.0
> plot(x,y,xlab="x”,

0.5

0.5
ylab="Sin x")

Sinus de x

0.0

0.0
y
-0.5

-0.5
> plot(x,y,type= "l",

-1.0

-1.0
main=“A Line") -6 -4 -2 0 2 4 6 -6 -4 -2 0 2 4 6

x x

> plot(x[seq(5,100,by=5)],

1.0
y[seq(5,100,by=5)],

0.5
y[seq(5, 100, by = 5)]

type= "b",axes=F)

0.0
y

-1.0
> plot(x,y,type="n",

-2.0
ylim=c(-2,1) -6 -4 -2 0 2 4 6

> par(mfrow=c(1,1))
x[seq(5, 100, by = 5)] x
Graphical Parameters of plot()

type = “c”: c =p (default), l, b,s,o,h,n.

pch=“+” : character or numbers 1 – 18
lty=1 : numbers
lwd=2 : numbers
axes = “L”: L= F, T
xlab =“string”, ylab=“string”
sub = “string”, main =“string”
xlim = c(lo,hi), ylim= c(lo,hi)
And some more.
Graphical Parameters of plot()

x <- 1:10
y <- 2*x + rnorm(10,0,1)
plot(x,y,type=“p”) #Try l,b,s,o,h,n
# axes=T, F
# xlab=“age”, ylab=“weight”
# sub=“sub title”, main=“main title”
# xlim=c(0,12), ylim=c(-1,12)
Other graphical functions
8
6

See also: 4
2
10

0 5
-2
-10
0
-5

barplot() 0 -5

image() 10
-10

hist()

120
pairs()

100
persp()

80
piechart()

dist

60
polygon()

40
library(modreg) 20

[Link]()
0

5 10 15 20 25

speed
Interactive Graphics Functions

 locator(n,type=“p”) :Waits for the user to select

locations on the current plot using the left mouse
button. This continues until n (default 500) points
have been selected.

 identify(x, y, labels) : Allow the user to highlight

any of the points defined by x and y.

 text(x,y,”Hey”): Write text at coordinate x,y.

Plots for Multivariate Data

pairs(stack.x)
x <- 1:20/20
y <- 1:20/20
z <-
outer(x,y,function(a,b){cos(10*a*b)/(1+a*b^2)})
contour(x,y,z)
persp(x,y,z)
image(x,y,z)
 Other graphical functions

> axis(1,at=c(2,4,5), Axis details (“ticks”, légende, …)

legend("A","B","C")) Use xaxt="n" ou yaxt="n" inside
plot()

> lines(x,y,…) Line plots

> abline(lsfit(x,y)) Add an adjustment

> abline(0,1) add a line of slope 1 and intercept 0

> legend(locator(1),…) Legends: very flexible

Histogram

 A histogram is a special kind of bar plot

 It allows you to visualize the distribution of values for a
numerical variable
 When drawn with a density scale:
 the AREA (NOT height) of each bar is the proportion of
observations in the interval
 the TOTAL AREA is 100% (or 1)
 R: making a histogram

 Type ?hist to view the help file

 Note some important arguments, esp breaks
 Simulate some data, make histograms varying the number of
bars (also called ‘bins’ or ‘cells’), e.g.
> par(mfrow=c(2,2)) # set up multiple plots
> simdata <-rchisq(100,8)
> hist(simdata) # default number of bins
> hist(simdata,breaks=2) # etc,4,20
R: setting your own breakpoints

> bps <- c(0,2,4,6,8,10,15,25)

> hist(simdata,breaks=bps)
Scatterplot

 A scatterplot is a standard two-dimensional (X,Y)

plot
 Used to examine the relationship between two
(continuous) variables
 It is often useful to plot values for a single
variable against the order or time the values were
obtained
 R: making a scatterplot

 Type ?plot to view the help file

 For now we will focus on simple plots, but R allows
extensive user control for highly customized plots
 Simulate a bivariate data set:
> z1 <- rnorm(50)
> z2 <- rnorm(50)
> rho <- .75 # (or any number between –1 and 1)
> x2<- rho*z1+sqrt(1-rho^2)*z2
> plot(z1,x2)
Statistical functions
 Lots of statistical functions

0.4
2
1  x  
1   

0.3
Normal distr 2  
f ( x |  , )  e

dnorm(x)
 2

0.2
PDF in point 2

0.1
> dnorm(2,mean=1,sd=2)
[1] 0.1760327 for X ~ N(1,4)

0.0
-4 -2 0 2 4

> qnorm(0.975) Quantile for

[1] 1.959964 the 0.975 for N~ (0,1)

> pnorm(c(2,3),mean=2) = P(X<2) and P(X<3), where X ~ N(2,1)

[1] 0.5000000 0.8413447
> [Link] <- rnorm(1000) Pseudo-random normally distributed numbers
> summary([Link])
Min. 1st Qu. Median Mean 3rd Qu. Max.
-3.418 -0.6625 -0.0429 -0.01797 0.6377 3.153
> sd([Link])
[1] 0.9881418
How to remember functions
For a normal distribution, the root is norm. Then add the letters
d density ( dnorm() )
p probability( pnorm() )
q quantiles ( qnorm() )
r pseudo-random ( rnorm() )

Distribution Root Argument

normal norm mean, sd, log
t (Student) t df, log
uniform unif min, max, log
F (Fisher) f df1, df2
2
chisq df, ncp, log
Binomial binom size, prob, log
exponential exp rate, log
Poisson pois lambda, log
...
 Hypotheses tests

[Link]()
Student (test t), determines if the averages of two populations are
statistically different.

[Link]()
hypothesis tests with proportions

Non-parametrical tests

[Link]() Kruskal-Wallis test (variance analysis)

[Link]() 2 test for convergence
[Link]() Kolmogorov-Smirnov test
...
Statistical models
Linear regression: lsfit() et lm()

lsfit() adjusment of regression models

Example – inclination of the Pisa tower

> year <- 75:87

> inclin <- c(642,644,656,667,673,688, 642 corresponds to
696,698,713,717,725,742,757) 2.9642m, the distance of a
point from its current position
> plot(year,inclin) and a vertical tower
> [Link] <- lsfit(year,inclin)
> [Link]([Link])
Residual Standard Error=4.181
R-Square=0.988
F-statistic (df=1, 11)=904.1198
p-value=0

Estimate [Link] t-value Pr(>|t|)

Intercept -61.1209 25.1298 -2.4322 0.0333
X 9.3187 0.3099 30.0686 0.0000

> abline([Link])
Data and models for Pisa tower

760
740
720
inclinaison

700
680
660
640

76 78 80 82 84 86

annee
Using lm() instead of lsfit()
> [Link] <- lm(inclin ~ year)
> [Link]
> summary([Link])
Call:
lm(formula = inclin ~ year)

Residuals:
Min 1Q Median 3Q Max
-5.9670 -3.0989 0.6703 2.3077 7.3956

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -61.1209 25.1298 -2.432 0.0333 *
year 9.3187 0.3099 30.069 6.5e-12 ***
---
Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1

Residual standard error: 4.181 on 11 degrees of freedom

Multiple R-Squared: 0.988, Adjusted R-squared: 0.9869
F-statistic: 904.1 on 1 and 11 DF, p-value: 6.503e-012
Generic functions ...
> residuals([Link])
1 2 3 4 ...
4.21978 -3.098901 -0.4175824 1.263736 ...

> fitted([Link])
1 2 3 4 ...
637.7802 647.0989 656.4176 665.7363 ...

> coef([Link])
(Intercept) annee
-61.12088 9.318681

> par(mfrow=c(2,3))
> plot([Link]) #cf. prochaine page
Diagnostics

Residuals vs Fitted Normal Q-Q plot

13 13

2
5

Standardized residuals

1
Residuals

0
-1
-5

8
8
11
11

640 660 680 700 720 740 -1.5 -0.5 0.0 0.5 1.0 1.5

Fitted values Theoretical Quantiles

Scale-Location plot Cook's distance plot

13
13
11 0.8
Standardized residuals

8
1.0

0.6
Cook's distance

0.4
0.5

1
11
0.2
0.0

0.0

640 660 680 700 720 740 2 4 6 8 10 12

Fitted values Obs. number

Multiple regression
> wheat <- [Link](yield=c(210,110,103,103,1,76,73,70,68,53,45,31),
temp=c(16.7,17.4,18.4,16.8,18.9,17.1,17.3,
18.2,21.3,21.2,20.7,18.5),
sunexp=c(30,42,47,47,43,41,48,44,43,50,56,60))

> [Link] <- lm(yield~temp+sunexp,

data=wheat)
> summary([Link],cor=F)
Residuals:
Min 1Q Median 3Q Max
-85.733 -11.117 6.411 16.476 53.375

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 420.660 131.292 3.204 0.0108 *
temperature -8.840 7.731 -1.143 0.2824
ensoleillement -3.880 1.704 -2.277 0.0488 *
---
Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1
...
Multiple regression diagnostics

> par(mfrow=c(2,2)) Residuals vs Fitted Normal Q-Q plot

> plot([Link])

2
1 1

50

Standardized residuals

1
Residuals

0
6

-50
6

-1
-2
5

-100
5

20 40 60 80 100 120 140 160 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5

Fitted values Theoretical Quantiles

Scale-Location plot Cook's distance plot

1.5

1.2
1
1
Standardized residuals

1.0
Cook's distance
1.0

0.8
6

0.6
0.5

0.4
5

0.2
11
0.0

0.0

20 40 60 80 100 120 140 160 2 4 6 8 10 12

Fitted values Obs. number

Hash tables
hash tables

 In vectors, lists, dataframes, arrays, elements are stored

one after another, and are accessed in that order by their
offset (or: index), which is an integer number.

 Sometimes, consecutive integer numbers are not the

“natural” way to access: e.g., gene names, oligo sequences

 E.g., if we want to look for a particular gene name in a long

list or data frame with tens of thousands of genes, the
linear search may be very slow.

 Solution: instead of list, use a hash table. It sorts, stores

and accesses its elements in a way similar to a telephone
book.
hash tables
In R, a hash table is the same as a workspace for
variables, which is the same as an environment.

> tab = [Link](hash=T)

> assign("btk", list(cloneid=682638,

fullname="Bruton agammaglobulinemia tyrosine kinase"),
env=tab)

> ls(env=tab)
[1] "btk"

> get("btk", env=tab)

$cloneid
[1] 682638
$fullname
[1] "Bruton agammaglobulinemia tyrosine kinase"
Object orientation
 Object orientation
.
 primitive (or: atomic) data types in R are:

 numeric (integer, double, complex)

 character
 logical
 function
 out of these, vectors, arrays, lists can be built
Object orientation

 Object: a collection of atomic variables and/or

other objects that belong together
 Example: a microarray experiment
 probe intensities
 patient data (tissue location, diagnosis, follow-up)
 gene data (sequence, IDs, annotation)

 Parlance:
 class: the “abstract” definition of it
 object: a concrete instance
 method: other word for ‘function’
 slot: a component of an object
Object orientation advantages

 Encapsulation (can use the objects and methods

someone else has written without having to care
about the internals)

 Generic functions (e.g. plot, print)

 Inheritance (hierarchical organization of

complexity)
 Object orientation
library('methods')
setClass('microarray', ## the class definition
representation( ## its slots
qua = 'matrix',
samples = 'character',
probes = 'vector'),
prototype = list( ## and default values
qua = matrix(nrow=0, ncol=0),
samples = character(0),
probes = character(0)))

dat = [Link]('../data/alizadeh/[Link]')
z = cbind(dat$CH1I, dat$CH2I)

setMethod('plot', ## overload generic function ‘plot’

signature(x='microarray'), ## for this new class
function(x, ...)
plot(x@qua, xlab=x@samples[1], ylab=x@samples[2], pch='.', log='xy'))

ma = new('microarray', ## instantiate (construct)

qua = z,
samples = c('brain','foot'))
plot(ma)
Object orientation in R

The plot([Link]) command is different from

plot(year,inclin) .

plot([Link])
R recognizes that [Link] is a “lm” object.
Uses [Link]() .

Most R functions are object-oriented.

For more details see ?methods and ?class

Importing/Exporting Data

 Importing data
 R can import data from other applications
 Packages are available to import microarray data, Excel
spreadsheets etc.
 The easiest way is to import tab delimited files
> [Link]<-[Link]("file",sep=",") *)
> SimpleData <- [Link](file =
"[Link] header = TRUE,
quote = "", sep = "\t", [Link]="")
 Exporting data
 R can also export data in various formats
 Tab delimited is the most common
> [Link](x, "filename") *)

*) make sure to include the path or

to first change the working directory
Getting help… and quitting

 Getting information about a specific command

> help(rnorm)
> ?rnorm
 Finding functions related to a key word
> [Link]("boxplot")
 Starting the R installation help pages
> [Link]()
 Quitting R
> q()
Getting help
Details about a specific command whose name you
know (input arguments, options, algorithm, results):

>? [Link]

or

>help([Link])
Resources

 Books  Online documentation

 Assigned text book  R Project documentation (
 For an extended list visit [Link]
[Link]  Manuals
ib/[Link]  FAQs

 …
 Mailing lists  Bioconductor documentation (
 R-help [Link]
(  Vignettes
[Link]
 Short Courses
html
)  …

 Bioconductor (  Google
[Link]
[Link]
)
 However, first
 read the posting guide/

general instructions and

 search archives