R Notebook

Arthmetic Operation

a = 10
b = 3

# Addition
res_add = a + b

# Sub
res_sub = a - b

# Multiplication
res_mult = a*b

# Division
res_div = a/b

# Modulo (reminder)
res_mod = a %% b

# Power
res_pow = a**b
res_pow2 = a^b

# Simplification
res = (5+3)*10 - ( (3-1) +4)/2

String

Conbine

seq1 = "ACTGCAATTTAC"
seq2 = "ACTTA"

combined_seq = paste(seq1, seq2)
print(combined_seq)

[1] "ACTGCAATTTAC ACTTA"

combined_seq = paste(seq1, seq2, sep = "")
print(combined_seq)

[1] "ACTGCAATTTACACTTA"

combined_seq = paste(seq1, seq2, sep = "-")
print(combined_seq)

[1] "ACTGCAATTTAC-ACTTA"

combined_seq = paste(seq1,seq1, seq2, seq2, sep = "-")
print(combined_seq)

[1] "ACTGCAATTTAC-ACTGCAATTTAC-ACTTA-ACTTA"

Substring

seq1 = "ACTGCAATTTAC"

sub = substr(seq1, 4, 8)
sub

[1] "GCAAT"

String length

seq3 = "ACTGCAATTTACACTGCAATTTACACTGCAATTTACACTGCAATTTACACTGCAATTTACACTGCAATTTACACTGCAATTTAC"

n = nchar(seq3)
n

[1] 84

nchar("ABCD")

[1] 4

Pattern matching

seq3 = "ACTGCAATTTACACTGCAATTTACACTGCAATTTACACTGCAATTTACACTGCAATTTACACTGCAATTTACACTGCAATTTAC"

p = "TTT"
grepl(p, seq3)

[1] TRUE

grepl("ZCVFJSP", seq3)

[1] FALSE

grepl("ACACTGCAATTTACACTGCAATTT", seq3)

[1] TRUE

occ = gregexpr(p, seq3)
occ

[[1]]
[1]  8 20 32 44 56 68 80
attr(,"match.length")
[1] 3 3 3 3 3 3 3
attr(,"index.type")
[1] "chars"
attr(,"useBytes")
[1] TRUE

sum(unlist(occ) != -1)

[1] 7

gregexpr("237489", seq3)

[[1]]
[1] -1
attr(,"match.length")
[1] -1
attr(,"index.type")
[1] "chars"
attr(,"useBytes")
[1] TRUE

Split string

seq4 = "gene1,gene2,gene3,gene4"

strsplit(seq4, split = ",")

[[1]]
[1] "gene1" "gene2" "gene3" "gene4"

seq4 = "gene1 - gene2 - gene3 - gene4"

strsplit(seq4, split = "-")

[[1]]
[1] "gene1 "  " gene2 " " gene3 " " gene4" 

Reverse string

library(stringi)
seq5 = "ACBDEFG"


stri_reverse(seq5)

[1] "GFEDBCA"

data_set = iris

Vector

Create

v = c( 10, 30, 68, "this", 89, "time" )
print(v)

[1] "10"   "30"   "68"   "this" "89"   "time"

Access [ ]

v[3]

[1] "68"

v[5]

[1] "89"

v[6]

[1] "time"

v[7]

[1] NA

v[1:3]

[1] "10" "30" "68"

v[2:4]

[1] "30"   "68"   "this"

v[2:10]

[1] "30"   "68"   "this" "89"   "time" NA     NA     NA     NA    

Insert element

v2 = c(v, 100)
v = c(v, 100)

v = c("start", v)
v

[1] "start" "10"    "30"    "68"    "this"  "89"    "time"  "100"  

v[1:3]

[1] "start" "10"    "30"   

v[4:8]

[1] "68"   "this" "89"   "time" "100" 

v = c(v[1:3], 200, v[4:8])
v

[1] "start" "10"    "30"    "200"   "68"    "this"  "89"    "time"  "100"  

Over-write

a = 200
a = 500

Sort

scores = c(10, 100, 50, 90, 89, 55)

sort(scores)

[1]  10  50  55  89  90 100

sort(scores, decreasing = TRUE)

[1] 100  90  89  55  50  10

?sort()

?match

match(100, scores)

[1] 2

match(90, scores)

[1] 4

match(1000, scores)

[1] NA

Conditional Selection

scores[ scores > 50 ]

[1] 100  90  89  55

scores[ scores >= 50 ]

[1] 100  50  90  89  55

scores[ scores < 50 ]

[1] 10

scores[ scores == 50 ]

[1] 50

scores[ scores == 1000 ]

numeric(0)

Find min

min(scores)

[1] 10

max

max(scores)

[1] 100

avg

mean(scores)

[1] 65.66667

sum

sum(scores)

[1] 394

length

length(scores)

[1] 6

394/6

[1] 65.66667

SD

sd(scores)

[1] 33.98039

variance

var(scores)

[1] 1154.667

standard error = sd/sqrt(n)

se = sd(scores) / sqrt(6)
se = sd(scores) / 6**0.5
se

[1] 13.87243

Quantiles

quantile(scores)

    0%    25%    50%    75%   100% 
 10.00  51.25  72.00  89.75 100.00 

Correlation

-1, +1 =>

age1 = c(60, 25, 50, 30, 27, 40)
age1

[1] 60 25 50 30 27 40

scores

[1]  10 100  50  90  89  55

cor(scores,age1)

[1] -0.9785945

age2 = c(100, 40, 30, 20, 100, 50)
cor(scores,age2)

[1] -0.3993987

cor(scores, scores)

[1] 1

age3 = c(30, 60, 35, 50, 45, 38)
cor(scores, age3)

[1] 0.9150097

Note: Gene expression heritibility and repitability

Delete element from a vec

scores

[1]  10 100  50  90  89  55

scores[-2]

[1] 10 50 90 89 55

Conditional statement (if else)

30 > 20

[1] TRUE

30 < 20

[1] FALSE

30 == 20

[1] FALSE

a = 30
b = 20

a > b

[1] TRUE

temp = 40

if (temp > 30) {
  print("This is a warm day!")
} else {
  print("This is a normal day")
}

[1] "This is a warm day!"

cal = "jodsjfs"
a = 10
b = 5

if (cal == "+"){
  print(a+b)
} else if (cal == "-") {
  print(a-b)
} else if (cal == "*") {
  print(a*b)
} else if (cal == "/") {
  print(a/b)
} else {
  print("Invalid")
}

[1] "Invalid"

scores

[1]  10 100  50  90  89  55

s = scores[4]

if (s > 50) {
  print("Pass!")
} else {
  print("Fail")
}

[1] "Pass!"

Loop

for (i in 1:10) {
  print(i)
}

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

scores

[1]  10 100  50  90  89  55

for (i in 1:10) {
  print(scores[i])
}

[1] 10
[1] 100
[1] 50
[1] 90
[1] 89
[1] 55
[1] NA
[1] NA
[1] NA
[1] NA

for (i in 1:length(scores)) {
  print(scores[i])
}

[1] 10
[1] 100
[1] 50
[1] 90
[1] 89
[1] 55

for (i in 1:length(scores)) {
  print(scores[i])
  
  s = scores[i]

  if (s > 50) {
    print("Pass!")
  } else {
    print("Fail")
  }
  
}

[1] 10
[1] "Fail"
[1] 100
[1] "Pass!"
[1] 50
[1] "Fail"
[1] 90
[1] "Pass!"
[1] 89
[1] "Pass!"
[1] 55
[1] "Pass!"

for (i in 1:length(scores)) {
  
  s = scores[i]

  if (s > 50) {
    cat(i, s, "Pass!\n")
  } else {
    cat(i, s, "Fail\n")
  }
  
}

1 10 Fail
2 100 Pass!
3 50 Fail
4 90 Pass!
5 89 Pass!
6 55 Pass!

scores

[1]  10 100  50  90  89  55