9.1 Vectors

A vector is a sequence of data elements from the same type.

329

45

12

28

9.1.1 Creating a vector

• Values are assigned to a vector using the c command (combining elements).

vector1 <- c(329, 45, 12, 28)

You can create an empty vector with:

vecempty <- vector()

• Create a sequence of consecutive numbers:

vecnum <- 10:16
# same as:
vecnum <- c(10, 11, 12, 13, 14, 15, 16)
# both ends (10 and 16) are included

• Character vectors: Each element is entered between (single or double) quotes.

mRNA

miRNA

snoRNA

lncRNA

mynames <- c("mRNA", "miRNA", "snoRNA", "lncRNA")

9.1.2 Vector manipulation

• A vector can be named: each element of the vector can be assigned a name (number or character)

names(vector1) <- c("mRNA", "miRNA", "snoRNA", "lncRNA")
# use an object which already contains a vector
names(vector1) <- mynames

• Get the length (number of elements) of a vector

length(vector1)

## [1] 4

• Extracting elements from vector a
  • extract elements using their position (index) in the vector:

  vecnum <- 10:16
  vecnum[1]

  ## [1] 10

  vecnum[c(1,3)]

  ## [1] 10 12

  vecnum[2:4]

  ## [1] 11 12 13

  • extract elements using their names:

  vector1["mRNA"]

  ## mRNA 
  ##  329

  vector1[c("miRNA", "lncRNA")]            

  ##  miRNA lncRNA 
  ##     45     28

• Reassigning a vector’s element

vector1[2] <- 31
vector1["miRNA"] <- 31

• Removing a vector’s element

vector1 <- vector1[-3]

• Show versus change

x[-2] x unchanged !

x <- x[-2] x reassigned !

9.1.3 Combining vectors

• From 2 vectors a and b you can create a vector d

v1 <- 2:5
v2 <- 4:6
v3 <- c(v1, v2)

The elements of v2 are added after the elements of v1

• Likewise, you can add elements at the end of a vector

v3 <- c(v3, 19)

9.1.4 Numeric vector manipulation

Logical operators

Operator	Description
<	less than
<=	less than or equal to
>	greater than
>=	greater than or equal to
==	exactly equal to
!=	not equal to
!x	not x
x | y	x OR y
x & y	x AND y

• Which elements of a are equal to 2?

a <- 1:5
a == 2

## [1] FALSE  TRUE FALSE FALSE FALSE

• Which elements of a are superior to 2?

a <- 1:5
a > 2

## [1] FALSE FALSE  TRUE  TRUE  TRUE

• Extract elements of a vector that comply with a condition:

a <- 1:5
a >= 2

## [1] FALSE  TRUE  TRUE  TRUE  TRUE

a[a >= 2]

## [1] 2 3 4 5

9.1.4.1 Operations on vectors

• Adding 2 to a vector adds 2 to each element of the vector:

a <- 1:5
a + 2

## [1] 3 4 5 6 7

Same goes for subtractions, multiplications and divisions…

• Multiplying a vector by another vector of equal length

a <- c(2, 4, 6)
b <- c(2, 3, 0)
a * b

## [1]  4 12  0

• Multiplying a vector by another shorter vector

a <- c(2, 4, 6, 3, 1)
b <- c(2, 3, 0)
a * b

## Warning in a * b: longer object length is not a multiple of shorter object
## length

## [1]  4 12  0  6  3

Vector a is “recycled” !

• Summary statistics

Function	Description
mean(x)	mean / average
median(x)	median
min(x)	minimum
max(x)	maximum
var(x)	variance
summary(x)	mean, median, min, max, quartiles

a <- c(1, 3, 12, 45, 3, 2)
summary(a)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    1.00    2.25    3.00   11.00    9.75   45.00

9.1.4.2 Comparing vectors

• The %in% operator

Which elements of a are also found in b ?

a <- 2:6
b <- 4:10
a %in% b

## [1] FALSE FALSE  TRUE  TRUE  TRUE

Retrieve actual elements of a that are found in b:

a <- 2:6
b <- 4:10
a[a %in% b]

## [1] 4 5 6

9.1.5 Character vector manipulation

Character vectors are manipulated similarly to numeric ones.

• The %in% operator:

k <- c("mRNA", "miRNA", "snoRNA", "RNA", "lincRNA")
p <- c("mRNA","lincRNA", "tRNA", "miRNA")
k %in% p

## [1]  TRUE  TRUE FALSE FALSE  TRUE

k[k %in% p]

## [1] "mRNA"    "miRNA"   "lincRNA"

• Select elements from vector m that are not exon

m <- c("exon", "intron", "exon")
m != "exon"

## [1] FALSE  TRUE FALSE

m[m != "exon"]

## [1] "intron"