getwd()

'/projects/fc96d042-48c2-4479-9884-fc9a89f4e931/Autumn2016/Week1'

setwd('~/Autumn2016')

objects()

'line'

x<-3
y<-10
z<-15

w<-(x+y+z)

return((y-x)/z)

x*y*z

sqrt(w)

w^4

a<-(z-x)
sqrt(a)

0.466666666666667

450

5.29150262212918

614656

3.46410161513775

myname <- "Joe"
Greeting <- "Hello my name is"
info <- "and I'm studying bioinformatics"
message <- paste(Greeting,myname,info,sep=" ")
print(message)

[1] "Hello my name is Joe and I'm studying bioinformatics"

55

10

x <- 1:10

assign('hello', 1:10)
print(hello)
sum(hello)
length(hello)
hello[5]
hello[3:8]

 [1]  1  2  3  4  5  6  7  8  9 10

55

10

5

1. 3
2. 4
3. 5
4. 6
5. 7
6. 8

assign('hello', 1:100)
print (hello)
sum(hello)

  [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18
 [19]  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36
 [37]  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54
 [55]  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72
 [73]  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90
 [91]  91  92  93  94  95  96  97  98  99 100

5050

sample(1:100, 12, replace=TRUE)
runif(4, min=10, max=900)
rnorm(10, mean=100, sd=50)

1. 85
2. 91
3. 98
4. 78
5. 70
6. 19
7. 22
8. 38
9. 15
10. 100
11. 69
12. 86

1. 798.076434270479
2. 899.334471581969
3. 327.451223421376
4. 772.472544419579

1. 80.8841282253673
2. 53.5188803726913
3. 135.198249783718
4. 80.0738107649404
5. 164.96422300186
6. 130.775733930803
7. 88.6591574989751
8. 98.6583436276265
9. 102.194391937866
10. 103.928272084579

x <- seq(length=15,from=2,by=2)
print(x)
length(x)
sum(x)
y <- seq(length=15,from=1,by=2)
print(y)
sum(y)
z <- seq(length=30,from=1,by=1)
print(z)
sum(z)
#The sum value of z is almost double that of x and y.

 [1]  2  4  6  8 10 12 14 16 18 20 22 24 26 28 30

15

240

 [1]  1  3  5  7  9 11 13 15 17 19 21 23 25 27 29

225

 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30

465

greeting <- "how's it going"
number <- 78953728462
message <- c(greeting,as.character(number))
print(message)

[1] "how's it going" "78953728462"   

Courses <- c("BMS", "APS", "MBB")
Numbers <- c(353,227,253)
message <- c(Courses,as.character(Numbers))
print(message)

Modules <- Map(c,Courses,Numbers)
print(Modules)

[1] "BMS" "APS" "MBB" "353" "227" "253"
$BMS
[1] "BMS" "353"

$APS
[1] "APS" "227"

$MBB
[1] "MBB" "253"

A<-1:50
dim(A)<-c(10,5)
A

B<-1:100
dim(B)<-c(2,50)
B

X<-51:100
dim(X)<-c(2,25)
X

1	11	21	31	41
2	12	22	32	42
3	13	23	33	43
4	14	24	34	44
5	15	25	35	45
6	16	26	36	46
7	17	27	37	47
8	18	28	38	48
9	19	29	39	49
10	20	30	40	50

1	3	5	7	9	11	13	15	17	19	⋯	81	83	85	87	89	91	93	95	97	99
2	4	6	8	10	12	14	16	18	20	⋯	82	84	86	88	90	92	94	96	98	100

51	53	55	57	59	61	63	65	67	69	⋯	81	83	85	87	89	91	93	95	97	99
52	54	56	58	60	62	64	66	68	70	⋯	82	84	86	88	90	92	94	96	98	100

Error in rbind(B, X): number of columns of matrices must match (see arg 2)
Traceback:

1. rbind(B, X)

matrix(1:40,nrow=4,ncol=10)

1	5	9	13	17	21	25	29	33	37
2	6	10	14	18	22	26	30	34	38
3	7	11	15	19	23	27	31	35	39
4	8	12	16	20	24	28	32	36	40

a <-c(matrix(1:5,nrow=1,ncol=5))
b <-c(matrix(6:10,nrow=1,ncol=5))
rbind(a,b)
cbind(a,b)

a	1	2	3	4	5
b	6	7	8	9	10

a	b
1	6
2	7
3	8
4	9
5	10

M <- matrix(1:20,nrow=4,ncol=5)
M

m <- matrix(1:4,nrow=2,ncol=2)

m[1,2] = 5
m[2,2] = 6

m

1	5	9	13	17
2	6	10	14	18
3	7	11	15	19
4	8	12	16	20

3	5
4	6

M <- matrix(1:20,nrow=4,ncol=5)
M

c <- matrix(1:8,nrow=2,ncol=4)

c[1,2] = 5
c[2,2] = 6

c[1,3] = 13
c[2,3] = 14

c[1,4] = 17
c[2,4] = 18

c

1	5	9	13	17
2	6	10	14	18
3	7	11	15	19
4	8	12	16	20

1	5	13	17
2	6	14	18

M <- matrix(1:20,nrow=4,ncol=5)
M

z <- matrix(1:5,nrow=1,ncol=5)

z[1,1] = 2
z[1,2] = 6
z[1,3] = 10
z[1,4] = 14
z[1,5] = 18

z

1	5	9	13	17
2	6	10	14	18
3	7	11	15	19
4	8	12	16	20

2

6

10

14

18

x <- matrix(1:9,nrow=3,ncol=3)
rownames(x)<-c('2013-2014','2014-2015','2015-2016')
colnames(x)<-c('BMS353','APS227','MBB253')

x[1,1] = sample(200:350, 1, replace=TRUE) 
x[1,2] = sample(200:350, 1, replace=TRUE)
x[1,3] = sample(200:350, 1, replace=TRUE)
x[2,1] = sample(200:350, 1, replace=TRUE)
x[2,2] = sample(200:350, 1, replace=TRUE)
x[2,3] = sample(200:350, 1, replace=TRUE)
x[3,1] = sample(200:350, 1, replace=TRUE)
x[3,2] = sample(200:350, 1, replace=TRUE)
x[3,3] = sample(200:350, 1, replace=TRUE)

x

S = x[1,1]+x[2,1]+x[3,1]
S

	BMS353	APS227	MBB253
2013-2014	220	290	255
2014-2015	282	316	229
2015-2016	289	294	257

791

a <- matrix(nrow=3,ncol=4)
b <- matrix(nrow=3,ncol=4)

a[1,1] = runif(1, min=1, max=100)
a[1,2] = runif(1, min=1, max=100)
a[1,3] = runif(1, min=1, max=100)
a[1,4] = runif(1, min=1, max=100)
a[2,1] = runif(1, min=1, max=100)
a[2,2] = runif(1, min=1, max=100)
a[2,3] = runif(1, min=1, max=100)
a[2,4] = runif(1, min=1, max=100)
a[3,1] = runif(1, min=1, max=100)
a[3,2] = runif(1, min=1, max=100)
a[3,3] = runif(1, min=1, max=100)
a[3,4] = runif(1, min=1, max=100)

b[1,1] = runif(1, min=1, max=100)
b[1,2] = runif(1, min=1, max=100)
b[1,3] = runif(1, min=1, max=100)
b[1,4] = runif(1, min=1, max=100)
b[2,1] = runif(1, min=1, max=100)
b[2,2] = runif(1, min=1, max=100)
b[2,3] = runif(1, min=1, max=100)
b[2,4] = runif(1, min=1, max=100)
b[3,1] = runif(1, min=1, max=100)
b[3,2] = runif(1, min=1, max=100)
b[3,3] = runif(1, min=1, max=100)
b[3,4] = runif(1, min=1, max=100)

a
b

a+b
a-b
a*b
sqrt(a)
sqrt(b)

79.83892	57.78864	11.25380	54.84656
69.32068	59.69974	10.52954	98.08338
46.72781	58.75983	30.67213	35.71172

75.18560	22.42895	21.58148	64.05056
39.11147	39.45464	74.43411	56.72634
18.86983	44.73048	11.13378	40.71691

155.02452	80.21759	32.83528	118.89712
108.43215	99.15438	84.96364	154.80972
65.59764	103.49031	41.80591	76.42863

4.653324	35.35968	-10.32768	-9.204006
30.209210	20.24509	-63.90457	41.357034
27.857983	14.02936	19.53835	-5.005190

6002.7371	1296.139	242.8736	3512.953
2711.2336	2355.432	783.7567	5563.911
881.7459	2628.356	341.4969	1454.071

8.935263	7.601884	3.354668	7.405846
8.325904	7.726560	3.244925	9.903705
6.835775	7.665496	5.538242	5.975929

8.670963	4.735922	4.645587	8.003160
6.253916	6.281293	8.627520	7.531689
4.343942	6.688085	3.336733	6.380981

myfunction <-function(x) {
    result <- var(x)
    return (result)
}

test<-myfunction(runif(12,min=100,max=200))
test

951.046695142479

x<-runif(12,min=30,max=40)
x 
var(x)

1. 38.5097428620793
2. 37.8460048581474
3. 37.1458997158334
4. 30.0948898890056
5. 31.5879360120744
6. 34.5735970232636
7. 38.4035057784058
8. 34.8107304493897
9. 38.0621735192835
10. 32.9206168651581
11. 37.5091786822304
12. 34.0149591094814

8.27199033970175

x <-c(5,4,3,2,1)
n <- length(x)
mx <- mean(x)

sum((((mx-5)^2)+((mx-4)^2)+((mx-3)^2)+((mx-2)^2)+((mx-1)^2))/(n-1))

2.5

myfunction <- function(answer, argument2){
    argument2 <- var(x)
    answer <-c(mean(x),sd(x))
    return (answer)
}

test<-myfunction(runif(54,min=100,max=578))
test

1. 163.371896767834
2. 77.1297505092774

Things Covered in This Week's Practical

• Creating vectors.
• Creating matrices.
• Carrying out functions on vectors and matrices.
• Binding matrices and vectors.
• Calculating variance using the formula provided and the var() function.
• Using myfunction to create user-defined functions.