R Notebook

Arethmetic 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

# Module (reminder)
res_mod = a %% b

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

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

String

Combine

seq1 = "ACTGAATTA"
seq2 = "ACTG"

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

[1] "ACTGAATTA ACTG"

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

[1] "ACTGAATTAACTG"

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

[1] "ACTGAATTA_ACTG"

Combined_seq = paste(seq1, seq1, seq2, seq2, sep = "_")
print(Combined_seq)

[1] "ACTGAATTA_ACTGAATTA_ACTG_ACTG"

substring

seq1 = "ACTGAATTA"
sub = substr(seq1, 4, 8)
sub

[1] "GAATT"

String length

seq3 = " ACTGAATTAACTGAATTAACTGAATTAACTGAATTAACTGAATTAACTGAATTAACTGAATTA"

n = nchar(seq3)
n

[1] 64

Pattern matching

seq3 = " ACTGAATTAACTGAATTAACTGAATTAACTGAATTAACTGAATTAACTGAATTAACTGAATTA"

p = "TT"
grep(p, seq3)

[1] 1

grepl(p, seq3)

[1] TRUE

grepl("cccc", seq3)

[1] FALSE

grepl("AACTGAATTAA", seq3)

[1] TRUE

Position finding

occ = gregexpr(p, seq3)
occ

[[1]]
[1]  8 17 26 35 44 53 62
attr(,"match.length")
[1] 2 2 2 2 2 2 2
attr(,"index.type")
[1] "chars"
attr(,"useBytes")
[1] TRUE

sum(unlist(occ) != -1)

[1] 7

gregexpr("234589", seq3)

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

How to split

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 = "ABCDEFG"

stri_reverse(seq5)

[1] "GFEDCBA"

data_set = iris

Vector

create

v = c(10, 30, 64, "this", 89, "time" )
print(v)

[1] "10"   "30"   "64"   "this" "89"   "time"

v1 = c(10, 30, 64, "this", 89, "time" )

Access [ ]

v[3]

[1] "64"

v[5]

[1] "89"

v[7]

[1] NA

v[1:3]

[1] "10" "30" "64"

v[2:4]

[1] "30"   "64"   "this"

v[2:10]

[1] "30"   "64"   "this" "89"   "time" NA     NA     NA     NA    

Insert element

v = c(v, 100)
v1 = c(v,200)

v1 = c("start", v)
v1

[1] "start" "10"    "30"    "64"    "this"  "89"    "time"  "100"  

v1[1:3]
v1[4:8]

v1 = c(v1[1:3], 300, v1[4:8])
v1

sorting (false means ascending,true means descending)

scores = c(10, 100, 50, 70, 90, 55, 89)
sort(scores)

[1]  10  50  55  70  89  90 100

sort(scores, decreasing = TRUE)

[1] 100  90  89  70  55  50  10

?sort()

match(100, scores)

[1] 2

match(70, scores)

[1] 4

match(1000, scores)

[1] NA

Conditional Selection

scores[scores > 50]

[1] 100  70  90  55  89

scores[scores >= 50]

[1] 100  50  70  90  55  89

scores[scores < 50]

[1] 10

scores[scores == 50]

[1] 50

scores[scores == 1000]

numeric(0)

find min,max

min(scores)

[1] 10

max(scores)

[1] 100

###avrg, sum

mean(scores)

[1] 66.28571

sum(scores)

[1] 464

length

length(scores)

[1] 7

SD

sd(scores)

[1] 31.06292

varience

var(scores)

[1] 964.9048

Standerd error = sd/sqrt(n)

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

[1] 12.68138

Quantiles

quantile(scores)

   0%   25%   50%   75%  100% 
 10.0  52.5  70.0  89.5 100.0 

correlation

-1, +1 =>

age1 = c(60, 25, 50, 30, 27, 40, 35)
age1

[1] 60 25 50 30 27 40 35

scores

[1]  10 100  50  70  90  55  89

cor(scores,age1)

[1] -0.9388972

age2 = c(100, 70, 60, 80, 60, 100, 90)
cor(scores,age2)

[1] -0.4987372

delete element from vec

scores

[1]  10 100  50  70  90  55  89

scores[-2]

[1] 10 50 70 90 55 89

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 = 25

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

[1] "This is a normal day"

cal = "-"
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] 5

scores

[1]  10 100  50  70  90  55  89

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

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

[1] 10
[1] 100
[1] 50
[1] 70
[1] 90
[1] 55
[1] 89
[1] NA
[1] NA
[1] NA

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

[1] 10
[1] 100
[1] 50
[1] 70
[1] 90
[1] 55
[1] 89

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] 70
[1] "pass!"
[1] 90
[1] "pass!"
[1] 55
[1] "pass!"
[1] 89
[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 70 pass!
5 90 pass!
6 55 pass!
7 89 pass!