9.1 Vectors

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

329 45 12 28

9.1.1 Creating a vector

  • Values are assigned to a vector using the c function (c for combining elements). Open and close the round brackets, and place the different elements, separated by commas.
vector1 <- c(329, 45, 12, 28)

You can create an empty vector with:

# empty vector
vecempty <- vector()
# empty numerical vector with 5 elements
vecnumempty <- vector(mode="numeric", length=5)
# empty character vector with 8 elements
veccharempty <- vector(mode="character", length=8)
  • Create a sequence of consecutive numbers:
vecnum <- 10:16
# shortcut for:
vecnum <- c(10, 11, 12, 13, 14, 15, 16)
# NOTES: 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")

HANDS-ON

  1. Create a vector (choose the name) that contains a sequence of number, from 3 to 8, both included.
  2. Create vector myfruits as:
myfruits <- c(apple, pear, orange)

What is happening? Why? Can you modify the line above so it doesn’t throw an error?

9.1.2 Vector manipulation

  • A vector can be named: each element of the vector can be assigned a name (number or character)
# our previous numerical vector
vector1 <- c(329, 45, 12, 28)
# assign names
names(vector1) <- c("mRNA", "miRNA", "snoRNA", "lncRNA")
# use an object which already contains a vector
mynames <- c("mRNA", "miRNA", "snoRNA", "lncRNA")
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: 
    vector1[1]
    ## mRNA 
##  329
    vector1[c(1,3)]
    ##   mRNA snoRNA 
##    329     12
    vector1[2:4]
    ##  miRNA snoRNA lncRNA 
##     45     12     28
    • extract elements using their names: 
    vector1["mRNA"]
    ## mRNA 
##  329
    vector1[c("miRNA", "lncRNA")]            
    ##  miRNA lncRNA 
##     45     28
  • Reassigning a vector’s element
# here we re-assign the 2nd element of vector1 with 31.
vector1[2] <- 31
vector1["miRNA"] <- 31
  • Removing a vector’s element
# here we remove the 3rd element of vector1
# show in the console vector1 without its 3rd element:
vector1[-3]
##   mRNA  miRNA lncRNA 
##    329     31     28
# reassign vector1 without its 3rd element
vector1 <- vector1[-3]
  • Show versus change

x[-2] x unchanged !

x <- x[-2] x reassigned !

9.1.3 Combining vectors

  • You can combine 2 (or more) vectors into one. Here, we combine v1 and v2 to create a vector v3
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
# extract the TRUE/FALSE vector
a >= 2
## [1] FALSE  TRUE  TRUE  TRUE  TRUE
# extract the actual sub-vector that complies the condition (TRUE values)
a[a >= 2]
## [1] 2 3 4 5
# count how many elements comply the condition
length(a[a >= 2])
## [1] 4

HANDS-ON

Given the following vector containing a group of people’s ages:

ages <- c(18, 32, 12, 34, 42, 32, 17, 56, 76, 10)
  1. How many people are over 18?
  2. How many people are under 60?
  3. How many people are between 25 and 45?

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 
k <- c(1, 3, 12, 45, 3, 2)
summary(k)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    1.00    2.25    3.00   11.00    9.75   45.00

HANDS-ON

Given our ages vector:

ages <- c(18, 32, 12, 34, 42, 32, 17, 56, 76, 10)
  1. What is the average/mean age?
  2. What is percentage of variation? It is defined as (standard deviation / mean) * 100.

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

Yields a TRUE/FALSE vector of the size of a.

Retrieve actual elements of a that are found in b:

a <- 2:6
b <- 4:10
a[a %in% b]
## [1] 4 5 6
  • Intersection:

Retrieve the intersection of 2 vectors:

intersect(a, b)
## [1] 4 5 6
  • Check if 2 vectors are exactly identical
identical(a, b)
## [1] FALSE

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"