R Notebook

Variable Type

# number var
num_var = 10
num_var2 = 20.5

# char var  -> letter, sentence
char_var = "This is a char var"
char_var2 = "This is another char var"

#logical var
logical1 = TRUE
logical2 = FALSE

#vector
num_vec = c( 1, 5,10,20, 50 )
fish_vec = c( "hilsha", "Ruhi", "telapia" )
fish_vec 

[1] "hilsha"  "Ruhi"    "telapia"

Arithmatic operation

a = 10
b = 5

# add
add = a+b

#minus
sub = a-b

# division
div = a/b

# multiplication
mult = a*b

# power
p = a^2

#modulo
m = a %% b
m2 = a %% 3

cat( add, sub, div, mult, p, m, m2)

15 5 2 50 100 0 1

combined calculation

c = (10 + (5-2) * 20 + (20-10))*10
c

[1] 800

string

concatenation or merge

var1 = "This is a variable"
var2 = "I am a variable"

combined = paste(var1, var2, var1, var2, sep = " - ")
combined

[1] "This is a variable - I am a variable - This is a variable - I am a variable"

var1 = "GTAC"
var2 = "ATGCA"
paste(var1, var2, sep = "")

[1] "GTACATGCA"

Segment

var = "GTACATGCAGTACATGCAGTACATGCAGTACATGCAGTACATGCAGTACATGCA"
substr(var, start = 12, stop = 16)

[1] "ACATG"

length

nchar(var)

[1] 54

pattern Exists?

gene_seq = "GTACATGCAGTACATGCAGTACATGCAGTACATGCAGTACATGCAGTACATGCA"
pattern1 = "ATGCE"
pattern2 = "TGCAGTA"

grepl(pattern1, gene_seq)

[1] FALSE

grepl(pattern2, gene_seq)

[1] TRUE

pattern matching

gene_seq = "GTACATGCAGTACATGCAGTACATGCAGTACATGCAGTACATGCAGTACATGCA"
pattern1 = "ATGCE"
pattern2 = "TGCAGTA"

matches = gregexpr(pattern2, gene_seq)
matches = unlist(matches)
matches

[1]  6 15 24 33 42

matches = gregexpr(pattern1, gene_seq)
matches = unlist(matches)
matches

[1] -1

Split

gene_seq = "GTACATGCAGT,ACATG,CAGTACAT,GCAGTACATGCAG,TACATGC,AGTACATGCA"
gene_vec = strsplit(gene_seq, split = " , ")
gene_vec

[[1]]
[1] "GTACATGCAGT,ACATG,CAGTACAT,GCAGTACATGCAG,TACATGC,AGTACATGCA"

gene_seq = "GTACATGCAGT ACATG CAGTACAT GCAGTACATGCAG TACATGC AGTACATGCA"
gene_vec = strsplit(gene_seq, split = " ")
gene_vec

[[1]]
[1] "GTACATGCAGT"   "ACATG"         "CAGTACAT"      "GCAGTACATGCAG" "TACATGC"       "AGTACATGCA"   

Reverse

library(stringi)
gene_seq = "GTACATGCAGT"
rev_gene_seq = stri_reverse(gene_seq)
rev_gene_seq 

[1] "TGACGTACATG"

library(stringi)
gene_seq = "This is a cat"
rev_gene_seq = stri_reverse(gene_seq)
rev_gene_seq 

[1] "tac a si sihT"

vector

ages = c(25, 45, 24, 67, 50, 40)
score = c(100, 70, 90, 50, 55, 79)

Index

ages[4]

[1] 67

score[1]

[1] 100

##remove

ages[-4]

[1] 25 45 24 50 40

ages = ages[-4]
ages

[1] 25 45 24